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APR Prediction Models
GAP (Generalized Aggregation Proneness)
ANuPP (Prediciton of Nucleating APRs)
V
L
AmY-Pred (Predicting antibody light chain aggregation)
Aggregation Kinetics Prediction Models
AggreRATE-Disc (Classifying Aggregating Point Mutation)
AggreRATE-Pred (Predicting Aggregation Rate for Point Mutation)
AbsoluRATE (Predicting Absolute aggregation rate)
Amylo-Pipe (Comprehensive aggregation prediction)
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APR Prediction Models:
GAP (Generalized Aggregation Proneness)
ANuPP (Prediciton of Nucleating APRs)
V
L
AmY-Pred (Predicting antibody light chain aggregation)
Aggregation Kinetics Prediction Models:
AggreRATE-Disc (Classifying Aggregating Point Mutation)
AggreRATE-Pred (Predicting Aggregation Rate for Point Mutation)
AbsoluRATE (Predicting Absolute aggregation rate)
Amylo-Pipe (Comprehensive aggregation prediction)
Structure database of aggregation related proteins and peptides
Select a Field to filter:
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Protein Name
Peptide Sequence
Entry ID
PDB ID
Method
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Protein/Peptide
Fibril
Aggregating complex
Inhibitor complex
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Protein complex
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Displaying 271 to 300 records out of 565 records fetched.
Entry
PDB ID
Protein
Name
Species
Length
Mutation(s)
Class
Type
Method
Resolution (
Å
)
PMID
S-0271
3NEO
Transthyretin
Homo sapiens
116
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
2.0
20937391
S-0272
3NES
Transthyretin
Homo sapiens
116
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
1.75
20937391
S-0273
3NEX
Transthyretin
Homo sapiens
116
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
1.7
20937391
S-0274
3NHC
Major prion protein
Homo sapiens
6
M129
Amyloid
Fibril
X-RAY DIFFRACTION
1.57
20685658
S-0275
3NHD
Major prion protein
Homo sapiens
6
V129
Amyloid
Fibril
X-RAY DIFFRACTION
1.92
20685658
S-0276
3NVE
Major prion protein
Mesocricetus auratus
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.7
21323366
S-0277
3NVF
Major prion protein
Homo sapiens
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.8
21323366
S-0278
3NVG
Major prion protein
Mus musculus
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.48
21323366
S-0279
3NVH
Major prion protein
Mus musculus
7
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.61
21323366
S-0280
3NX0
Cystatin-C
Homo sapiens
120
V57N
Non-amyloid
Protein
X-RAY DIFFRACTION
2.04
21074623
S-0281
3OVJ
Amyloid-beta A4 protein
synthetic construct
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.8
21695112
S-0282
3OVL
Microtubule-associated protein tau
Homo sapiens
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.81
21695112
S-0283
3OW9
Amyloid-beta A4 protein
synthetic construct
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.8
21949245
S-0284
3PPD
Prostatic acid phosphatase
Homo sapiens
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.5
21677644
S-0285
3PS8
Cystatin-C
Homo sapiens
120
L68V
Amyloid
Protein
X-RAY DIFFRACTION
2.55
S-0286
3PZZ
Amyloid-beta A4 protein
Homo sapiens
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.29
21949245
S-0287
3Q25
alpha-synuclein
390
No
Non-amyloid
Protein
X-RAY DIFFRACTION
1.9
21462277
S-0288
3Q26
alpha-synuclein
404
No
Non-amyloid
Protein
X-RAY DIFFRACTION
1.54
21462277
S-0289
3Q27
alpha-synuclein
397
No
Non-amyloid
Protein
X-RAY DIFFRACTION
1.3
21462277
S-0290
3Q28
alpha-synuclein
393
No
Non-amyloid
Protein
X-RAY DIFFRACTION
1.6
21462277
S-0291
3Q29
alpha-synuclein
390
No
Non-amyloid
Protein
X-RAY DIFFRACTION
2.3
21462277
S-0292
3Q2X
Amyloid-beta A4 protein
Homo sapiens
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.45
21949245
S-0293
3Q9G
Tau protein
10
No
Amyloid
Fibril
X-RAY DIFFRACTION
2.05
21473620
S-0294
3Q9H
Amyloid-Beta
10
No
Amyloid
Fibril
X-RAY DIFFRACTION
2.25
21473620
S-0295
3Q9I
Amyloid-Beta
10
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.99
21473620
S-0296
3Q9J
Amyloid-Beta
10
No
Amyloid
Fibril
X-RAY DIFFRACTION
2.55
21473620
S-0297
3SGM
Alpha-crystallin B chain
Homo sapiens
11
K11V-Br2
Amyloid
Fibril
X-RAY DIFFRACTION
1.7
22403391
S-0298
3SGN
Alpha-crystallin B chain
Homo sapiens
11
K11V-Br8
Amyloid
Fibril
X-RAY DIFFRACTION
2.81
22403391
S-0299
3SGO
Alpha-crystallin B chain
Homo sapiens
11
K11V
Amyloid
Fibril
X-RAY DIFFRACTION
2.56
22403391
S-0300
3SGP
Alpha-crystallin B chain
Homo sapiens
11
K11V, V2L
Amyloid
Fibril
X-RAY DIFFRACTION
1.4
22403391
Entry:S-0271
PDB ID: 3NEO
CSV
JSON
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Structure
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View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
I
N
V
A
V
H
V
F
R
25
26
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
E
S
G
E
L
H
G
L
T
50
51
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
K
S
Y
W
K
A
L
G
I
75
76
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
G
P
R
R
Y
T
I
A
A
100
101
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
116
Chain 2
1
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
I
N
V
A
V
H
V
F
R
25
26
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
E
S
G
E
L
H
G
L
T
50
51
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
K
S
Y
W
K
A
L
G
I
75
76
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
G
P
R
R
Y
T
I
A
A
100
101
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
116
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Wild type human transthyretin (TTR) complexed with GC-24 (TTRwt:GC-24)
They characterized the interactions of the synthetic triiodo L-thyronine analogs and thyroid hormone nuclear receptor TR-Beta-selective agonists GC-1 and GC-24 with the wild type and V30M variant of human transthyretin (TTR). The data indicate that both GC-1 and GC-24 bind to TTR in a non-cooperative manner and are good inhibitors of TTR aggregation
Literature
PMID:
20937391
Author(s):
Trivella, D.B., Sairre, M.I., Foguel, D., Lima, L.M., Polikarpov, I.
Reference:
J Struct Biol. 2011 Feb;173(2):323-32.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
116
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
3NEO
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
TRANSPORT PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.0
R free:
0.22
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
G24
A
C24 H24 O4
376.45
[4-(3-BENZYL-4-HYDROXYBENZYL)-3,5-DIMETHYLPHENOXY]ACETIC ACID
Cc1cc(cc(c1Cc2ccc(c(c2)Cc3ccccc3)O)C)OCC(=O)O
JYHIGYLGYNCMGI-UHFFFAOYSA-N
G24
B
C24 H24 O4
376.45
[4-(3-BENZYL-4-HYDROXYBENZYL)-3,5-DIMETHYLPHENOXY]ACETIC ACID
Cc1cc(cc(c1Cc2ccc(c(c2)Cc3ccccc3)O)C)OCC(=O)O
JYHIGYLGYNCMGI-UHFFFAOYSA-N
Entry:S-0272
PDB ID: 3NES
CSV
JSON
Close ×
Structure
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View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
I
N
V
A
M
H
V
F
R
25
26
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
E
S
G
E
L
H
G
L
T
50
51
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
K
S
Y
W
K
A
L
G
I
75
76
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
G
P
R
R
Y
T
I
A
A
100
101
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
116
Chain 2
1
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
I
N
V
A
M
H
V
F
R
25
26
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
E
S
G
E
L
H
G
L
T
50
51
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
K
S
Y
W
K
A
L
G
I
75
76
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
G
P
R
R
Y
T
I
A
A
100
101
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
116
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
V30M mutant human transthyretin (TTR) complexed with GC-1 (V30M:GC-1)
They characterized the interactions of the synthetic triiodo L-thyronine analogs and thyroid hormone nuclear receptor TR-Beta-selective agonists GC-1 and GC-24 with the wild type and V30M variant of human transthyretin (TTR). The data indicate that both GC-1 and GC-24 bind to TTR in a non-cooperative manner and are good inhibitors of TTR aggregation
Literature
PMID:
20937391
Author(s):
Trivella, D.B., Sairre, M.I., Foguel, D., Lima, L.M., Polikarpov, I.
Reference:
J Struct Biol. 2011 Feb;173(2):323-32.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
116
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
3NES
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
TRANSPORT PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.75
R free:
0.223
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
B72
A
C20 H24 O4
328.4
{4-[4-hydroxy-3-(1-methylethyl)benzyl]-3,5-dimethylphenoxy}acetic acid
Cc1cc(cc(c1Cc2ccc(c(c2)C(C)C)O)C)OCC(=O)O
QNAZTOHXCZPOSA-UHFFFAOYSA-N
GOL
A
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
B72
B
C20 H24 O4
328.4
{4-[4-hydroxy-3-(1-methylethyl)benzyl]-3,5-dimethylphenoxy}acetic acid
Cc1cc(cc(c1Cc2ccc(c(c2)C(C)C)O)C)OCC(=O)O
QNAZTOHXCZPOSA-UHFFFAOYSA-N
GOL
B
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Entry:S-0273
PDB ID: 3NEX
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
I
N
V
A
M
H
V
F
R
25
26
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
E
S
G
E
L
H
G
L
T
50
51
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
K
S
Y
W
K
A
L
G
I
75
76
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
G
P
R
R
Y
T
I
A
A
100
101
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
116
Chain 2
1
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
I
N
V
A
M
H
V
F
R
25
26
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
E
S
G
E
L
H
G
L
T
50
51
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
K
S
Y
W
K
A
L
G
I
75
76
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
G
P
R
R
Y
T
I
A
A
100
101
L
L
S
P
Y
S
Y
S
T
T
A
V
V
T
N
P
116
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
V30M mutant human transthyretin (TTR) complexed with GC-24 (V30M:GC-24)
They characterized the interactions of the synthetic triiodo L-thyronine analogs and thyroid hormone nuclear receptor TR-Beta-selective agonists GC-1 and GC-24 with the wild type and V30M variant of human transthyretin (TTR). The data indicate that both GC-1 and GC-24 bind to TTR in a non-cooperative manner and are good inhibitors of TTR aggregation
Literature
PMID:
20937391
Author(s):
Trivella, D.B., Sairre, M.I., Foguel, D., Lima, L.M., Polikarpov, I.
Reference:
J Struct Biol. 2011 Feb;173(2):323-32.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
116
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
3NEX
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
TRANSPORT PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.7
R free:
0.207
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
G24
A
C24 H24 O4
376.45
[4-(3-BENZYL-4-HYDROXYBENZYL)-3,5-DIMETHYLPHENOXY]ACETIC ACID
Cc1cc(cc(c1Cc2ccc(c(c2)Cc3ccccc3)O)C)OCC(=O)O
JYHIGYLGYNCMGI-UHFFFAOYSA-N
GOL
A
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
G24
B
C24 H24 O4
376.45
[4-(3-BENZYL-4-HYDROXYBENZYL)-3,5-DIMETHYLPHENOXY]ACETIC ACID
Cc1cc(cc(c1Cc2ccc(c(c2)Cc3ccccc3)O)C)OCC(=O)O
JYHIGYLGYNCMGI-UHFFFAOYSA-N
GOL
B
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Entry:S-0274
PDB ID: 3NHC
CSV
JSON
Close ×
Structure
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View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
Y
M
L
G
S
6
Chain 2
1
G
Y
M
L
G
S
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
GYMLGS segment 127-132 from human prion with M129
"They determined crystal structures of prion segments having either Met or Val at residue 129. These 6-residue segments of PrP centered on residue 129 are ""steric zippers,"" pairs of interacting Beta-sheets. Both structures of these ""homozygous steric zippers"" reveal direct intermolecular interactions between Met or Val in one sheet and the identical residue in the mating sheet."
Literature
PMID:
20685658
Author(s):
Apostol, M.I., Sawaya, M.R., Cascio, D., Eisenberg, D.
Reference:
J Biol Chem. 2010 Sep 24;285(39):29671-5.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Major prion protein
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
M129
E.C. Number:
UniProt ID:
P04156
Keyword(s):
Major prion protein
Structure Information
PDB ID:
3NHC
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 12-mer - A12
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.57
R free:
0.253
Entry:S-0275
PDB ID: 3NHD
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
Y
V
L
G
S
6
Chain 2
1
G
Y
V
L
G
S
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
GYVLGS segment 127-132 from human prion with V129
"we determined crystal structures of prion segments having either Met or Val at residue 129. These 6-residue segments of PrP centered on residue 129 are ""steric zippers,"" pairs of interacting Beta-sheets. Both structures of these ""homozygous steric zippers"" reveal direct intermolecular interactions between Met or Val in one sheet and the identical residue in the mating sheet."
Literature
PMID:
20685658
Author(s):
Apostol, M.I., Sawaya, M.R., Cascio, D., Eisenberg, D.
Reference:
J Biol Chem. 2010 Sep 24;285(39):29671-5.
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Protein Information
Protein Name:
Major prion protein
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
V129
E.C. Number:
UniProt ID:
P04156
Keyword(s):
Major prion protein
Structure Information
PDB ID:
3NHD
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 12-mer - A12
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.92
R free:
0.261
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
ACY
A
C2 H4 O2
60.05
ACETIC ACID
CC(=O)O
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Entry:S-0276
PDB ID: 3NVE
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Sequence & Sec. Str.
Chain 1
1
M
M
H
F
G
N
6
Chain 2
1
M
M
H
F
G
N
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
MMHFGN segment 138-143 from Syrian Hamster prion
Prion represents a unique class of pathogens devoid of nucleic acid. The deadly diseases transmitted by it between members of one species and, in certain instances, to members of other species present a public health concern. Here we present three X-ray atomic structures of the same segment from human, mouse, and hamster PrP, which is critical for forming amyloid and confers species specificity in PrP seeding experiments. The structures reveal that different sequences encode different steric zippers and suggest that the degree of dissimilarity of these zipper structures gives rise to transmission barriers in prion disease,
Literature
PMID:
21323366
Author(s):
Apostol, M.I., Wiltzius, J.J., Sawaya, M.R., Cascio, D., Eisenberg, D.
Reference:
Biochemistry. 2011 Apr 5;50(13):2456-63.
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Protein Information
Protein Name:
Major prion protein
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Mesocricetus auratus
Mutation(s):
No
E.C. Number:
UniProt ID:
P04273
Keyword(s):
Major prion protein
Structure Information
PDB ID:
3NVE
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 12-mer - A12
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.7
R free:
0.26899999
Entry:S-0277
PDB ID: 3NVF
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Sequence & Sec. Str.
Chain 1
1
I
I
H
F
G
S
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
IIHFGS segment 138-143 from human prion
Prion represents a unique class of pathogens devoid of nucleic acid. The deadly diseases transmitted by it between members of one species and, in certain instances, to members of other species present a public health concern. Here we present three X-ray atomic structures of the same segment from human, mouse, and hamster PrP, which is critical for forming amyloid and confers species specificity in PrP seeding experiments. The structures reveal that different sequences encode different steric zippers and suggest that the degree of dissimilarity of these zipper structures gives rise to transmission barriers in prion disease,
Literature
PMID:
21323366
Author(s):
Apostol, M.I., Wiltzius, J.J., Sawaya, M.R., Cascio, D., Eisenberg, D.
Reference:
Biochemistry. 2011 Apr 5;50(13):2456-63.
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Entry:
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Structure:
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Contact Network:
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Protein Information
Protein Name:
Major prion protein
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P04156
Keyword(s):
Major prion protein
Structure Information
PDB ID:
3NVF
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 10-mer - A10
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.8
R free:
0.226
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
MPD
A
C6 H14 O2
118.17
(4S)-2-METHYL-2,4-PENTANEDIOL
C[C@@H](CC(C)(C)O)O
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Entry:S-0278
PDB ID: 3NVG
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Sequence & Sec. Str.
Chain 1
1
M
I
H
F
G
N
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
MIHFGN segment 137-142 from mouse prion
Prion represents a unique class of pathogens devoid of nucleic acid. The deadly diseases transmitted by it between members of one species and, in certain instances, to members of other species present a public health concern. Here we present three X-ray atomic structures of the same segment from human, mouse, and hamster PrP, which is critical for forming amyloid and confers species specificity in PrP seeding experiments. The structures reveal that different sequences encode different steric zippers and suggest that the degree of dissimilarity of these zipper structures gives rise to transmission barriers in prion disease,
Literature
PMID:
21323366
Author(s):
Apostol, M.I., Wiltzius, J.J., Sawaya, M.R., Cascio, D., Eisenberg, D.
Reference:
Biochemistry. 2011 Apr 5;50(13):2456-63.
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Entry:
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Protein Information
Protein Name:
Major prion protein
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Mus musculus
Mutation(s):
No
E.C. Number:
UniProt ID:
P04925
Keyword(s):
Major prion protein
Structure Information
PDB ID:
3NVG
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 10-mer - A10
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.48
R free:
0.205
Entry:S-0279
PDB ID: 3NVH
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Sequence & Sec. Str.
Chain 1
1
M
I
H
F
G
N
D
7
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
MIHFGND segment 137-143 from mouse prion
Prion represents a unique class of pathogens devoid of nucleic acid. The deadly diseases transmitted by it between members of one species and, in certain instances, to members of other species present a public health concern. Here we present three X-ray atomic structures of the same segment from human, mouse, and hamster PrP, which is critical for forming amyloid and confers species specificity in PrP seeding experiments. The structures reveal that different sequences encode different steric zippers and suggest that the degree of dissimilarity of these zipper structures gives rise to transmission barriers in prion disease,
Literature
PMID:
21323366
Author(s):
Apostol, M.I., Wiltzius, J.J., Sawaya, M.R., Cascio, D., Eisenberg, D.
Reference:
Biochemistry. 2011 Apr 5;50(13):2456-63.
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Entry:
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Structure:
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Contact Network:
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Protein Information
Protein Name:
Major prion protein
Alternative Name:
Gene Name:
Sequence Length:
7
Species:
Mus musculus
Mutation(s):
No
E.C. Number:
UniProt ID:
P04925
Keyword(s):
Major prion protein
Structure Information
PDB ID:
3NVH
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 10-mer - A10
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.61
R free:
0.19699999
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
TFA
A
C2 H F3 O2
114.02
trifluoroacetic acid
C(=O)(C(F)(F)F)O
DTQVDTLACAAQTR-UHFFFAOYSA-N
Entry:S-0280
PDB ID: 3NX0
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
S
S
P
G
K
P
P
R
L
V
G
G
P
M
D
A
S
V
E
E
E
G
V
R
R
25
26
A
L
D
F
A
V
G
E
Y
N
K
A
S
N
D
M
Y
H
S
R
A
L
Q
V
V
50
51
R
A
R
K
Q
I
N
A
G
V
N
Y
F
L
D
V
E
L
G
R
T
T
C
T
K
75
76
T
Q
P
N
L
D
N
C
P
F
H
D
Q
P
H
L
K
R
K
A
F
C
S
F
Q
100
101
I
Y
A
V
P
W
Q
G
T
M
T
L
S
K
S
T
C
Q
D
A
120
Chain 2
1
S
S
P
G
K
P
P
R
L
V
G
G
P
M
D
A
S
V
E
E
E
G
V
R
R
25
26
A
L
D
F
A
V
G
E
Y
N
K
A
S
N
D
M
Y
H
S
R
A
L
Q
V
V
50
51
R
A
R
K
Q
I
N
A
G
V
N
Y
F
L
D
V
E
L
G
R
T
T
C
T
K
75
76
T
Q
P
N
L
D
N
C
P
F
H
D
Q
P
H
L
K
R
K
A
F
C
S
F
Q
100
101
I
Y
A
V
P
W
Q
G
T
M
T
L
S
K
S
T
C
Q
D
A
120
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Hinge-loop mutation can be used to control 3D domain swapping and amyloidogenesis of human cystatin C
They mutated cystatin C with the smallest possible structural intervention, that is a single-point mutation replacing hydrophobic V57 from the L1 loop by polar asparagine, known as a stabilizer of a Beta-turn motif. V57N hCC mutant occurred to be stable in its monomeric form and crystallized as a monomer, revealing typical cystatin fold with a five-stranded antiparallel Beta-sheet wrapped around an Alpha-helix.
Literature
PMID:
21074623
Author(s):
Orlikowska, M., Jankowska, E., Kolodziejczyk, R., Jaskolski, M., Szymanska, A.
Reference:
J Struct Biol. 2011 Feb;173(2):406-13.
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Protein Information
Protein Name:
Cystatin-C
Alternative Name:
Cystatin-3, Gamma-trace, Neuroendocrine basic polypeptide, Post-gamma-globulin
Gene Name:
CST3
Sequence Length:
120
Species:
Homo sapiens
Mutation(s):
V57N
E.C. Number:
UniProt ID:
P01034
Keyword(s):
Cystatin-C
Structure Information
PDB ID:
3NX0
Amyloid Category:
Non-amyloid
Type:
Protein
Global Stoichiometry:
PDB Classification:
HYDROLASE INHIBITOR
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.04
R free:
0.225
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
SO4
A
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
SO4
B
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
Entry:S-0281
PDB ID: 3OVJ
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Sequence & Sec. Str.
Chain 1
1
K
L
V
F
F
A
6
Chain 2
1
K
L
V
F
F
A
6
Chain 3
1
K
L
V
F
F
A
6
Chain 4
1
K
L
V
F
F
A
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Structure of an amyloid forming peptide KLVFFA from amyloid beta in complex with orange G
They present atomic structures of fiber-forming segments of proteins involved in Alzheimer's disease in complex with small molecule binders, determined by X-ray microcrystallography. The fiber-like complexes consist of pairs of Beta-sheets, with small molecules binding between the sheets, roughly parallel to the fiber axis. The structures suggest that apolar molecules drift along the fiber, consistent with the observation of nonspecific binding to a variety of amyloid proteins.
Literature
PMID:
21695112
Author(s):
Landau, M., Sawaya, M.R., Faull, K.F., Laganowsky, A., Jiang, L., Sievers, S.A., Liu, J., Barrio, J.R., Eisenberg, D.
Reference:
PLoS Biol. 2011 Jun;9(6):e1001080.
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Protein Information
Protein Name:
Amyloid-beta A4 protein
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
synthetic construct
Mutation(s):
No
E.C. Number:
UniProt ID:
P05067
Keyword(s):
KLVFFA hexapeptide segment from Amyloid beta
Structure Information
PDB ID:
3OVJ
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.8
R free:
0.22
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
ORA
B
C16 H12 N2 O7 S2
408.41
7-hydroxy-8-[(E)-phenyldiazenyl]naphthalene-1,3-disulfonic acid
c1ccc(cc1)/N=N/c2c(ccc3c2c(cc(c3)S(=O)(=O)O)S(=O)(=O)O)O
MPVDXIMFBOLMNW-ISLYRVAYSA-N
ORA
D
C16 H12 N2 O7 S2
408.41
7-hydroxy-8-[(E)-phenyldiazenyl]naphthalene-1,3-disulfonic acid
c1ccc(cc1)/N=N/c2c(ccc3c2c(cc(c3)S(=O)(=O)O)S(=O)(=O)O)O
MPVDXIMFBOLMNW-ISLYRVAYSA-N
Entry:S-0282
PDB ID: 3OVL
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Sequence & Sec. Str.
Chain 1
1
V
Q
I
V
Y
K
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Structure of an amyloid forming peptide VQIVYK from the TAU protein in complex with orange G
They present atomic structures of fiber-forming segments of proteins involved in Alzheimer's disease in complex with small molecule binders, determined by X-ray microcrystallography. The fiber-like complexes consist of pairs of Beta-sheets, with small molecules binding between the sheets, roughly parallel to the fiber axis. The structures suggest that apolar molecules drift along the fiber, consistent with the observation of nonspecific binding to a variety of amyloid proteins.
Literature
PMID:
21695112
Author(s):
Landau, M., Sawaya, M.R., Faull, K.F., Laganowsky, A., Jiang, L., Sievers, S.A., Liu, J., Barrio, J.R., Eisenberg, D.
Reference:
PLoS Biol. 2011 Jun;9(6):e1001080.
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Protein Information
Protein Name:
Microtubule-associated protein tau
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P10636
Keyword(s):
Microtubule-associated protein
Structure Information
PDB ID:
3OVL
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 6-mer - A6
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.81
R free:
0.259
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
ACY
A
C2 H4 O2
60.05
ACETIC ACID
CC(=O)O
QTBSBXVTEAMEQO-UHFFFAOYSA-N
ORA
A
C16 H12 N2 O7 S2
408.41
7-hydroxy-8-[(E)-phenyldiazenyl]naphthalene-1,3-disulfonic acid
c1ccc(cc1)/N=N/c2c(ccc3c2c(cc(c3)S(=O)(=O)O)S(=O)(=O)O)O
MPVDXIMFBOLMNW-ISLYRVAYSA-N
ZN
A
Zn 2
65.41
ZINC ION
[Zn+2]
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Entry:S-0283
PDB ID: 3OW9
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Sequence & Sec. Str.
Chain 1
1
K
L
V
F
F
A
6
Chain 2
1
K
L
V
F
F
A
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Structure of an amyloid forming peptide KLVFFA from amyloid beta, alternate polymorph II
ABeta molecules form Beta-sheet containing structures that assemble into a variety of polymorphic oligomers, protofibers, and fibers that exhibit a range of lifetimes and cellular toxicities. This polymorphic nature of ABeta has frustrated its biophysical characterization, its structural determination, and our understanding of its pathological mechanism. They determined eight new microcrystal structures of fiber-forming segments of ABeta. These structures, all of short, self-complementing pairs of Beta-sheets termed steric zippers, reveal a variety of modes of self-association of ABeta.
Literature
PMID:
21949245
Author(s):
Colletier, J.P., Laganowsky, A., Landau, M., Zhao, M., Soriaga, A.B., Goldschmidt, L., Flot, D., Cascio, D., Sawaya, M.R., Eisenberg, D.
Reference:
Proc Natl Acad Sci U S A. 2011 Oct 11;108(41):16938-43.
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Protein Information
Protein Name:
Amyloid-beta A4 protein
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
synthetic construct
Mutation(s):
No
E.C. Number:
UniProt ID:
P05067
Keyword(s):
KLVFFA hexapeptide segment from Amyloid beta
Structure Information
PDB ID:
3OW9
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 12-mer - A12
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.8
R free:
0.257
Entry:S-0284
PDB ID: 3PPD
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Sequence & Sec. Str.
Chain 1
1
G
G
V
L
V
N
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
GGVLVN segment from Human Prostatic Acid Phosphatase Residues 260-265, involved in Semen-Derived Enhancer of Viral Infection
They used GGVLVN as a template for inhibitor design, which is the steric-zipper structure of the peptide segment GGVLVN from the amyloid fiber formed by 248-PAP-286, a proteolytic fragment of prostatic acid phosphatase (PAP), a protein abundant in semen. 248-PAP-286 fibers enhance HIV infection by orders of magnitude in cell culture studies, while the monomeric peptide is inactive.
Literature
PMID:
21677644
Author(s):
Sievers, S.A., Karanicolas, J., Chang, H.W., Zhao, A., Jiang, L., Zirafi, O., Stevens, J.T., Munch, J., Baker, D., Eisenberg, D.
Reference:
Nature. 2011 Jun 15;475(7354):96-100.
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Protein Information
Protein Name:
Prostatic acid phosphatase
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P15309
Keyword(s):
GGVLVN peptide, amyloid forming segment
Structure Information
PDB ID:
3PPD
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 6-mer - A6
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.5
R free:
0.21899999
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
ACY
A
C2 H4 O2
60.05
ACETIC ACID
CC(=O)O
QTBSBXVTEAMEQO-UHFFFAOYSA-N
ZN
A
Zn 2
65.41
ZINC ION
[Zn+2]
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Entry:S-0285
PDB ID: 3PS8
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
S
S
P
G
K
P
P
R
L
V
G
G
P
M
D
A
S
V
E
E
E
G
V
R
R
25
26
A
L
D
F
A
V
G
E
Y
N
K
A
S
N
D
M
Y
H
S
R
A
L
Q
V
V
50
51
R
A
R
K
Q
I
V
A
G
V
N
Y
F
L
D
V
E
V
G
R
T
T
C
T
K
75
76
T
Q
P
N
L
D
N
C
P
F
H
D
Q
P
H
L
K
R
K
A
F
C
S
F
Q
100
101
I
Y
A
V
P
W
Q
G
T
M
T
L
S
K
S
T
C
Q
D
A
120
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of L68V mutant of human cystatin C
Crystal structure of L68V mutant of human cystatin C. Compared to the wild-type cystatin C, L68V shows increased tendency for dimerization, even under milder destabilization conditions.
Literature
PMID:
Author(s):
Orlikowska, M., Szymanska, A., Borek, D., Otwinowski, Z., Skowron, P., Jankowska, E.
Reference:
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Structure:
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Protein Information
Protein Name:
Cystatin-C
Alternative Name:
Cystatin-3, Gamma-trace, Neuroendocrine basic polypeptide, Post-gamma-globulin
Gene Name:
CST3
Sequence Length:
120
Species:
Homo sapiens
Mutation(s):
L68V
E.C. Number:
UniProt ID:
P01034
Keyword(s):
Cystatin-C
Structure Information
PDB ID:
3PS8
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
HYDROLASE INHIBITOR
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.55
R free:
0.251
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
ACT
A
C2 H3 O2 -1
59.04
ACETATE ION
CC(=O)[O-]
QTBSBXVTEAMEQO-UHFFFAOYSA-M
PEG
A
C4 H10 O3
106.12
DI(HYDROXYETHYL)ETHER
C(COCCO)O
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Entry:S-0286
PDB ID: 3PZZ
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
A
I
I
G
L
6
Chain 2
1
G
A
I
I
G
L
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Structure of an amyloid forming peptide GAIIGL (29-34) from amyloid beta
ABeta molecules form Beta-sheet containing structures that assemble into a variety of polymorphic oligomers, protofibers, and fibers that exhibit a range of lifetimes and cellular toxicities. This polymorphic nature of ABeta has frustrated its biophysical characterization, its structural determination, and our understanding of its pathological mechanism. They determined eight new microcrystal structures of fiber-forming segments of ABeta. These structures, all of short, self-complementing pairs of Beta-sheets termed steric zippers, reveal a variety of modes of self-association of ABeta.
Literature
PMID:
21949245
Author(s):
Colletier, J.P., Laganowsky, A., Landau, M., Zhao, M., Soriaga, A.B., Goldschmidt, L., Flot, D., Cascio, D., Sawaya, M.R., Eisenberg, D.
Reference:
Proc Natl Acad Sci U S A. 2011 Oct 11;108(41):16938-43.
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Protein Information
Protein Name:
Amyloid-beta A4 protein
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P05067
Keyword(s):
Amyloid beta A4 protein
Structure Information
PDB ID:
3PZZ
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 12-mer - A12
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.29
R free:
0.196
Entry:S-0287
PDB ID: 3Q25
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
M
K
I
E
E
G
K
L
V
I
W
I
N
G
D
K
G
Y
N
G
L
A
E
V
G
25
26
K
K
F
E
K
D
T
G
I
K
V
T
V
E
H
P
D
K
L
E
E
K
F
P
Q
50
51
V
A
A
T
G
D
G
P
D
I
I
F
W
A
H
D
R
F
G
G
Y
A
Q
S
G
75
76
L
L
A
E
I
T
P
D
K
A
F
Q
D
K
L
Y
P
F
T
W
D
A
V
R
Y
100
101
N
G
K
L
I
A
Y
P
I
A
V
E
A
L
S
L
I
Y
N
K
D
L
L
P
N
125
126
P
P
K
T
W
E
E
I
P
A
L
D
K
E
L
K
A
K
G
K
S
A
L
M
F
150
151
N
L
Q
E
P
Y
F
T
W
P
L
I
A
A
D
G
G
Y
A
F
K
Y
E
N
G
175
176
K
Y
D
I
K
D
V
G
V
D
N
A
G
A
K
A
G
L
T
F
L
V
D
L
I
200
201
K
N
K
H
M
N
A
D
T
D
Y
S
I
A
E
A
A
F
N
K
G
E
T
A
M
225
226
T
I
N
G
P
W
A
W
S
N
I
D
T
S
K
V
N
Y
G
V
T
V
L
P
T
250
251
F
K
G
Q
P
S
K
P
F
V
G
V
L
S
A
G
I
N
A
A
S
P
N
K
E
275
276
L
A
K
E
F
L
E
N
Y
L
L
T
D
E
G
L
E
A
V
N
K
D
K
P
L
300
301
G
A
V
A
L
K
S
Y
E
E
E
L
A
K
D
P
R
I
A
A
T
M
E
N
A
325
326
Q
K
G
E
I
M
P
N
I
P
Q
M
S
A
F
W
Y
A
V
R
T
A
V
I
N
350
351
A
A
S
G
R
Q
T
V
D
E
A
L
K
D
A
Q
T
N
S
S
S
M
D
V
F
375
376
M
K
G
L
S
K
A
K
E
G
V
V
A
A
A
390
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of human alpha-synuclein (1-19) fused to maltose binding protein (MBP)
They use maltose-binding protein (MBP) as a carrier to crystallize segments of Alpha-synuclein. From crystal structures of fusions between MBP and four segments of Alpha-synuclein, They have been able to trace a virtual model of the first 72 residues of Alpha-synuclein. Instead of a mostly Alpha-helical conformation observed in the lipid environment, our crystal structures show Alpha-helices only at residues 1-13 and 20-34. The remaining segments are extended loops or coils. All of the predicted fiber-forming segments based on the 3D profile method are in extended conformations. Crystallized constructs showed fiber-like nano-crystals that are much thicker than typical amyloid fibrils without visible ThT fluorescence. (space group: P 4(3) 2(1) 2)
Literature
PMID:
21462277
Author(s):
Zhao, M., Cascio, D., Sawaya, M.R., Eisenberg, D.
Reference:
Protein Sci. 2011 Jun;20(6):996-1004.
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Entry:
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Structure:
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Contact Network:
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Protein Information
Protein Name:
alpha-synuclein
Alternative Name:
P0AEX9:, MMBP, Maltodextrin-binding protein, Maltose-binding protein, P37840:, Non-A beta component of AD amyloid, Non-A4 component of amyloid precursor
Gene Name:
P0AEX9:, malE, b4034, JW3994, P37840:, SNCA, NACP, PARK1
Sequence Length:
390
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Maltose-binding periplasmic protein/alpha-synuclein chimeric protein, fiber-like nano-crystals (without visible ThT fluorescence)
Structure Information
PDB ID:
3Q25
Amyloid Category:
Non-amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
SUGAR BINDING PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.9
R free:
0.196
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
GOL
A
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MAL
A
C12 H22 O11
342.3
MALTOSE
C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)O)CO)O)O)O)O
GUBGYTABKSRVRQ-ASMJPISFSA-N
SO4
A
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
Entry:S-0288
PDB ID: 3Q26
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JSON
Close ×
Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
M
K
I
E
E
G
K
L
V
I
W
I
N
G
D
K
G
Y
N
G
L
A
E
V
G
25
26
K
K
F
E
K
D
T
G
I
K
V
T
V
E
H
P
D
K
L
E
E
K
F
P
Q
50
51
V
A
A
T
G
D
G
P
D
I
I
F
W
A
H
D
R
F
G
G
Y
A
Q
S
G
75
76
L
L
A
E
I
T
P
D
K
A
F
Q
D
K
L
Y
P
F
T
W
D
A
V
R
Y
100
101
N
G
K
L
I
A
Y
P
I
A
V
E
A
L
S
L
I
Y
N
K
D
L
L
P
N
125
126
P
P
K
T
W
E
E
I
P
A
L
D
K
E
L
K
A
K
G
K
S
A
L
M
F
150
151
N
L
Q
E
P
Y
F
T
W
P
L
I
A
A
D
G
G
Y
A
F
K
Y
E
N
G
175
176
K
Y
D
I
K
D
V
G
V
D
N
A
G
A
K
A
G
L
T
F
L
V
D
L
I
200
201
K
N
K
H
M
N
A
D
T
D
Y
S
I
A
E
A
A
F
N
K
G
E
T
A
M
225
226
T
I
N
G
P
W
A
W
S
N
I
D
T
S
K
V
N
Y
G
V
T
V
L
P
T
250
251
F
K
G
Q
P
S
K
P
F
V
G
V
L
S
A
G
I
N
A
A
S
P
N
K
E
275
276
L
A
K
E
F
L
E
N
Y
L
L
T
D
E
G
L
E
A
V
N
K
D
K
P
L
300
301
G
A
V
A
L
K
S
Y
E
E
E
L
A
K
D
P
R
I
A
A
T
M
E
N
A
325
326
Q
K
G
E
I
M
P
N
I
P
Q
M
S
A
F
W
Y
A
V
R
T
A
V
I
N
350
351
A
A
S
G
R
Q
T
V
D
E
A
L
K
D
A
Q
T
N
S
S
S
K
A
K
E
375
376
G
V
V
A
A
A
E
K
T
K
Q
G
V
A
E
A
A
G
K
T
K
E
G
V
L
400
401
Y
V
G
S
404
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Cyrstal structure of human alpha-synuclein (10-42) fused to maltose binding protein (MBP)
They use maltose-binding protein (MBP) as a carrier to crystallize segments of Alpha-synuclein. From crystal structures of fusions between MBP and four segments of Alpha-synuclein, They have been able to trace a virtual model of the first 72 residues of Alpha-synuclein. Instead of a mostly Alpha-helical conformation observed in the lipid environment, our crystal structures show Alpha-helices only at residues 1-13 and 20-34. The remaining segments are extended loops or coils. All of the predicted fiber-forming segments based on the 3D profile method are in extended conformations. Crystallized constructs showed fiber-like nano-crystals that are much thicker than typical amyloid fibrils without visible ThT fluorescence.
Literature
PMID:
21462277
Author(s):
Zhao, M., Cascio, D., Sawaya, M.R., Eisenberg, D.
Reference:
Protein Sci. 2011 Jun;20(6):996-1004.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
alpha-synuclein
Alternative Name:
P0AEX9:, MMBP, Maltodextrin-binding protein, Maltose-binding protein, P37840:, Non-A beta component of AD amyloid, Non-A4 component of amyloid precursor
Gene Name:
P0AEX9:, malE, b4034, JW3994, P37840:, SNCA, NACP, PARK1
Sequence Length:
404
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Maltose-binding periplasmic protein/alpha-synuclein chimeric protein, fiber-like nano-crystals (without visible ThT fluorescence)
Structure Information
PDB ID:
3Q26
Amyloid Category:
Non-amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
SUGAR BINDING PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.54
R free:
0.183
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
GOL
A
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MAL
A
C12 H22 O11
342.3
MALTOSE
C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)O)CO)O)O)O)O
GUBGYTABKSRVRQ-ASMJPISFSA-N
SO4
A
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
Entry:S-0289
PDB ID: 3Q27
CSV
JSON
Close ×
Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
M
K
I
E
E
G
K
L
V
I
W
I
N
G
D
K
G
Y
N
G
L
A
E
V
G
25
26
K
K
F
E
K
D
T
G
I
K
V
T
V
E
H
P
D
K
L
E
E
K
F
P
Q
50
51
V
A
A
T
G
D
G
P
D
I
I
F
W
A
H
D
R
F
G
G
Y
A
Q
S
G
75
76
L
L
A
E
I
T
P
D
K
A
F
Q
D
K
L
Y
P
F
T
W
D
A
V
R
Y
100
101
N
G
K
L
I
A
Y
P
I
A
V
E
A
L
S
L
I
Y
N
K
D
L
L
P
N
125
126
P
P
K
T
W
E
E
I
P
A
L
D
K
E
L
K
A
K
G
K
S
A
L
M
F
150
151
N
L
Q
E
P
Y
F
T
W
P
L
I
A
A
D
G
G
Y
A
F
K
Y
E
N
G
175
176
K
Y
D
I
K
D
V
G
V
D
N
A
G
A
K
A
G
L
T
F
L
V
D
L
I
200
201
K
N
K
H
M
N
A
D
T
D
Y
S
I
A
E
A
A
F
N
K
G
E
T
A
M
225
226
T
I
N
G
P
W
A
W
S
N
I
D
T
S
K
V
N
Y
G
V
T
V
L
P
T
250
251
F
K
G
Q
P
S
K
P
F
V
G
V
L
S
A
G
I
N
A
A
S
P
N
K
E
275
276
L
A
K
E
F
L
E
N
Y
L
L
T
D
E
G
L
E
A
V
N
K
D
K
P
L
300
301
G
A
V
A
L
K
S
Y
E
E
E
L
A
K
D
P
R
I
A
A
T
M
E
N
A
325
326
Q
K
G
E
I
M
P
N
I
P
Q
M
S
A
F
W
Y
A
V
R
T
A
V
I
N
350
351
A
A
S
G
R
Q
T
V
D
E
A
L
K
D
A
Q
T
N
S
S
S
K
T
K
E
375
376
G
V
L
Y
V
G
S
K
T
K
E
G
V
V
H
G
V
A
T
V
A
E
397
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Cyrstal structure of human alpha-synuclein (32-57) fused to maltose binding protein (MBP)
They use maltose-binding protein (MBP) as a carrier to crystallize segments of Alpha-synuclein. From crystal structures of fusions between MBP and four segments of Alpha-synuclein, They have been able to trace a virtual model of the first 72 residues of Alpha-synuclein. Instead of a mostly Alpha-helical conformation observed in the lipid environment, our crystal structures show Alpha-helices only at residues 1-13 and 20-34. The remaining segments are extended loops or coils. All of the predicted fiber-forming segments based on the 3D profile method are in extended conformations. Crystallized constructs showed fiber-like nano-crystals that are much thicker than typical amyloid fibrils without visible ThT fluorescence.
Literature
PMID:
21462277
Author(s):
Zhao, M., Cascio, D., Sawaya, M.R., Eisenberg, D.
Reference:
Protein Sci. 2011 Jun;20(6):996-1004.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
alpha-synuclein
Alternative Name:
P0AEX9:, MMBP, Maltodextrin-binding protein, Maltose-binding protein, P37840:, Non-A beta component of AD amyloid, Non-A4 component of amyloid precursor
Gene Name:
P0AEX9:, malE, b4034, JW3994, P37840:, SNCA, NACP, PARK1
Sequence Length:
397
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Maltose-binding periplasmic protein/alpha-synuclein chimeric protein, fiber-like nano-crystals (without visible ThT fluorescence)
Structure Information
PDB ID:
3Q27
Amyloid Category:
Non-amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
SUGAR BINDING PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.3
R free:
0.156
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
GOL
A
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MAL
A
C12 H22 O11
342.3
MALTOSE
C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)O)CO)O)O)O)O
GUBGYTABKSRVRQ-ASMJPISFSA-N
SO4
A
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
Entry:S-0290
PDB ID: 3Q28
CSV
JSON
Close ×
Structure
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View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
M
K
I
E
E
G
K
L
V
I
W
I
N
G
D
K
G
Y
N
G
L
A
E
V
G
25
26
K
K
F
E
K
D
T
G
I
K
V
T
V
E
H
P
D
K
L
E
E
K
F
P
Q
50
51
V
A
A
T
G
D
G
P
D
I
I
F
W
A
H
D
R
F
G
G
Y
A
Q
S
G
75
76
L
L
A
E
I
T
P
D
K
A
F
Q
D
K
L
Y
P
F
T
W
D
A
V
R
Y
100
101
N
G
K
L
I
A
Y
P
I
A
V
E
A
L
S
L
I
Y
N
K
D
L
L
P
N
125
126
P
P
K
T
W
E
E
I
P
A
L
D
K
E
L
K
A
K
G
K
S
A
L
M
F
150
151
N
L
Q
E
P
Y
F
T
W
P
L
I
A
A
D
G
G
Y
A
F
K
Y
E
N
G
175
176
K
Y
D
I
K
D
V
G
V
D
N
A
G
A
K
A
G
L
T
F
L
V
D
L
I
200
201
K
N
K
H
M
N
A
D
T
D
Y
S
I
A
E
A
A
F
N
K
G
E
T
A
M
225
226
T
I
N
G
P
W
A
W
S
N
I
D
T
S
K
V
N
Y
G
V
T
V
L
P
T
250
251
F
K
G
Q
P
S
K
P
F
V
G
V
L
S
A
G
I
N
A
A
S
P
N
K
E
275
276
L
A
K
E
F
L
E
N
Y
L
L
T
D
E
G
L
E
A
V
N
K
D
K
P
L
300
301
G
A
V
A
L
K
S
Y
E
E
E
L
A
K
D
P
R
I
A
A
T
M
E
N
A
325
326
Q
K
G
E
I
M
P
N
I
P
Q
M
S
A
F
W
Y
A
V
R
T
A
V
I
N
350
351
A
A
S
G
R
Q
T
V
D
E
A
L
K
D
A
Q
T
N
S
S
S
K
T
K
E
375
376
Q
V
T
N
V
G
G
A
V
V
T
G
V
T
A
V
A
Q
393
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Cyrstal structure of human alpha-synuclein (58-79) fused to maltose binding protein (MBP)
They use maltose-binding protein (MBP) as a carrier to crystallize segments of Alpha-synuclein. From crystal structures of fusions between MBP and four segments of Alpha-synuclein, They have been able to trace a virtual model of the first 72 residues of Alpha-synuclein. Instead of a mostly Alpha-helical conformation observed in the lipid environment, our crystal structures show Alpha-helices only at residues 1-13 and 20-34. The remaining segments are extended loops or coils. All of the predicted fiber-forming segments based on the 3D profile method are in extended conformations. Crystallized constructs showed fiber-like nano-crystals that are much thicker than typical amyloid fibrils without visible ThT fluorescence.
Literature
PMID:
21462277
Author(s):
Zhao, M., Cascio, D., Sawaya, M.R., Eisenberg, D.
Reference:
Protein Sci. 2011 Jun;20(6):996-1004.
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Entry:
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Structure:
PDB
CIF
FASTA
Contact Network:
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JSON
Protein Information
Protein Name:
alpha-synuclein
Alternative Name:
P0AEX9:, MMBP, Maltodextrin-binding protein, Maltose-binding protein, P37840:, Non-A beta component of AD amyloid, Non-A4 component of amyloid precursor
Gene Name:
P0AEX9:, malE, b4034, JW3994, P37840:, SNCA, NACP, PARK1
Sequence Length:
393
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Maltose-binding periplasmic protein/alpha-synuclein chimeric protein, fiber-like nano-crystals (without visible ThT fluorescence)
Structure Information
PDB ID:
3Q28
Amyloid Category:
Non-amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
SUGAR BINDING PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.6
R free:
0.17300000
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
MAL
A
C12 H22 O11
342.3
MALTOSE
C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)O)CO)O)O)O)O
GUBGYTABKSRVRQ-ASMJPISFSA-N
SO4
A
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
Entry:S-0291
PDB ID: 3Q29
CSV
JSON
Close ×
Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
M
K
I
E
E
G
K
L
V
I
W
I
N
G
D
K
G
Y
N
G
L
A
E
V
G
25
26
K
K
F
E
K
D
T
G
I
K
V
T
V
E
H
P
D
K
L
E
E
K
F
P
Q
50
51
V
A
A
T
G
D
G
P
D
I
I
F
W
A
H
D
R
F
G
G
Y
A
Q
S
G
75
76
L
L
A
E
I
T
P
D
K
A
F
Q
D
K
L
Y
P
F
T
W
D
A
V
R
Y
100
101
N
G
K
L
I
A
Y
P
I
A
V
E
A
L
S
L
I
Y
N
K
D
L
L
P
N
125
126
P
P
K
T
W
E
E
I
P
A
L
D
K
E
L
K
A
K
G
K
S
A
L
M
F
150
151
N
L
Q
E
P
Y
F
T
W
P
L
I
A
A
D
G
G
Y
A
F
K
Y
E
N
G
175
176
K
Y
D
I
K
D
V
G
V
D
N
A
G
A
K
A
G
L
T
F
L
V
D
L
I
200
201
K
N
K
H
M
N
A
D
T
D
Y
S
I
A
E
A
A
F
N
K
G
E
T
A
M
225
226
T
I
N
G
P
W
A
W
S
N
I
D
T
S
K
V
N
Y
G
V
T
V
L
P
T
250
251
F
K
G
Q
P
S
K
P
F
V
G
V
L
S
A
G
I
N
A
A
S
P
N
K
E
275
276
L
A
K
E
F
L
E
N
Y
L
L
T
D
E
G
L
E
A
V
N
K
D
K
P
L
300
301
G
A
V
A
L
K
S
Y
E
E
E
L
A
K
D
P
R
I
A
A
T
M
E
N
A
325
326
Q
K
G
E
I
M
P
N
I
P
Q
M
S
A
F
W
Y
A
V
R
T
A
V
I
N
350
351
A
A
S
G
R
Q
T
V
D
E
A
L
K
D
A
Q
T
N
S
S
S
M
D
V
F
375
376
M
K
G
L
S
K
A
K
E
G
V
V
A
A
A
390
Chain 2
1
M
K
I
E
E
G
K
L
V
I
W
I
N
G
D
K
G
Y
N
G
L
A
E
V
G
25
26
K
K
F
E
K
D
T
G
I
K
V
T
V
E
H
P
D
K
L
E
E
K
F
P
Q
50
51
V
A
A
T
G
D
G
P
D
I
I
F
W
A
H
D
R
F
G
G
Y
A
Q
S
G
75
76
L
L
A
E
I
T
P
D
K
A
F
Q
D
K
L
Y
P
F
T
W
D
A
V
R
Y
100
101
N
G
K
L
I
A
Y
P
I
A
V
E
A
L
S
L
I
Y
N
K
D
L
L
P
N
125
126
P
P
K
T
W
E
E
I
P
A
L
D
K
E
L
K
A
K
G
K
S
A
L
M
F
150
151
N
L
Q
E
P
Y
F
T
W
P
L
I
A
A
D
G
G
Y
A
F
K
Y
E
N
G
175
176
K
Y
D
I
K
D
V
G
V
D
N
A
G
A
K
A
G
L
T
F
L
V
D
L
I
200
201
K
N
K
H
M
N
A
D
T
D
Y
S
I
A
E
A
A
F
N
K
G
E
T
A
M
225
226
T
I
N
G
P
W
A
W
S
N
I
D
T
S
K
V
N
Y
G
V
T
V
L
P
T
250
251
F
K
G
Q
P
S
K
P
F
V
G
V
L
S
A
G
I
N
A
A
S
P
N
K
E
275
276
L
A
K
E
F
L
E
N
Y
L
L
T
D
E
G
L
E
A
V
N
K
D
K
P
L
300
301
G
A
V
A
L
K
S
Y
E
E
E
L
A
K
D
P
R
I
A
A
T
M
E
N
A
325
326
Q
K
G
E
I
M
P
N
I
P
Q
M
S
A
F
W
Y
A
V
R
T
A
V
I
N
350
351
A
A
S
G
R
Q
T
V
D
E
A
L
K
D
A
Q
T
N
S
S
S
M
D
V
F
375
376
M
K
G
L
S
K
A
K
E
G
V
V
A
A
A
390
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Cyrstal structure of human alpha-synuclein (1-19) fused to maltose binding protein (MBP); in space group P212121
They use maltose-binding protein (MBP) as a carrier to crystallize segments of Alpha-synuclein. From crystal structures of fusions between MBP and four segments of Alpha-synuclein, They have been able to trace a virtual model of the first 72 residues of Alpha-synuclein. Instead of a mostly Alpha-helical conformation observed in the lipid environment, our crystal structures show Alpha-helices only at residues 1-13 and 20-34. The remaining segments are extended loops or coils. All of the predicted fiber-forming segments based on the 3D profile method are in extended conformations. Crystallized constructs showed fiber-like nano-crystals that are much thicker than typical amyloid fibrils without visible ThT fluorescence. space group: P 2(1) 2(1) 2(1)).
Literature
PMID:
21462277
Author(s):
Zhao, M., Cascio, D., Sawaya, M.R., Eisenberg, D.
Reference:
Protein Sci. 2011 Jun;20(6):996-1004.
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Entry:
CSV
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Structure:
PDB
CIF
FASTA
Contact Network:
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JSON
Protein Information
Protein Name:
alpha-synuclein
Alternative Name:
P0AEX9:, MMBP, Maltodextrin-binding protein, Maltose-binding protein, P37840:, Non-A beta component of AD amyloid, Non-A4 component of amyloid precursor
Gene Name:
P0AEX9:, malE, b4034, JW3994, P37840:, SNCA, NACP, PARK1
Sequence Length:
390
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Maltose-binding periplasmic protein/alpha-synuclein chimeric protein, fiber-like nano-crystals (without visible ThT fluorescence)
Structure Information
PDB ID:
3Q29
Amyloid Category:
Non-amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
SUGAR BINDING PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.3
R free:
0.23199999
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
GOL
A
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MAL
A
C12 H22 O11
342.3
MALTOSE
C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)O)CO)O)O)O)O
GUBGYTABKSRVRQ-ASMJPISFSA-N
SO4
A
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
C
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MAL
C
C12 H22 O11
342.3
MALTOSE
C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)O)CO)O)O)O)O
GUBGYTABKSRVRQ-ASMJPISFSA-N
SO4
C
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
Entry:S-0292
PDB ID: 3Q2X
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Sequence & Sec. Str.
Chain 1
1
N
K
G
A
I
I
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Structure of an amyloid forming peptide NKGAII (residues 27-32) from amyloid beta
ABeta molecules form Beta-sheet containing structures that assemble into a variety of polymorphic oligomers, protofibers, and fibers that exhibit a range of lifetimes and cellular toxicities. This polymorphic nature of ABeta has frustrated its biophysical characterization, its structural determination, and our understanding of its pathological mechanism. They determined eight new microcrystal structures of fiber-forming segments of ABeta. These structures, all of short, self-complementing pairs of Beta-sheets termed steric zippers, reveal a variety of modes of self-association of ABeta.
Literature
PMID:
21949245
Author(s):
Colletier, J.P., Laganowsky, A., Landau, M., Zhao, M., Soriaga, A.B., Goldschmidt, L., Flot, D., Cascio, D., Sawaya, M.R., Eisenberg, D.
Reference:
Proc Natl Acad Sci U S A. 2011 Oct 11;108(41):16938-43.
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Entry:
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Structure:
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Protein Information
Protein Name:
Amyloid-beta A4 protein
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P05067
Keyword(s):
Amyloid beta A4 protein
Structure Information
PDB ID:
3Q2X
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 6-mer - A6
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.45
R free:
0.259
Entry:S-0293
PDB ID: 3Q9G
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Sequence & Sec. Str.
Chain 1
1
V
Q
I
V
Y
A
X
K
L
A
10
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
VQIVY segment from Alzheimer's tau displayed on 42-membered macrocycle scaffold
They explore oligomer structure using a model system: macrocyclic peptides. Key amyloidogenic sequences from ABeta and tau were incorporated into macrocycles, thereby restraining them to Beta-strands, but limiting the growth of the oligomers so they may crystallize and cannot fibrillate. Oligomers reveal tetrameric interfaces in which Beta-sheet dimers pair together by highly complementary, dry interfaces, analogous to steric zippers found in fibers, suggesting a common structure for amyloid oligomers and fibers. In amyloid fibers, the axes of the paired sheets are either parallel or antiparallel, whereas the oligomeric interfaces display a variety of sheet-to-sheet pairing angles, offering a structural explanation for the heterogeneity of amyloid oligomers.
Literature
PMID:
21473620
Author(s):
Liu, C., Sawaya, M.R., Cheng, P.N., Zheng, J., Nowick, J.S., Eisenberg, D.
Reference:
J Am Chem Soc. 2011 May 4;133(17):6736-44.
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Entry:
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Structure:
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Protein Information
Protein Name:
Tau protein
Alternative Name:
Gene Name:
Sequence Length:
10
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Cyclic pseudo-peptide VQIV(4BF)(ORN)(HAO)KL(ORN)
Structure Information
PDB ID:
3Q9G
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.05
R free:
0.203
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
4BF
A
C9 H10 Br N O2
244.09
4-BROMO-L-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)Br
PEMUHKUIQHFMTH-QMMMGPOBSA-N
ACY
A
C2 H4 O2
60.05
ACETIC ACID
CC(=O)O
QTBSBXVTEAMEQO-UHFFFAOYSA-N
GOL
A
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
HAO
A
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
A
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
Entry:S-0294
PDB ID: 3Q9H
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
L
V
F
F
A
A
X
L
K
A
10
Chain 2
1
L
V
F
F
A
A
X
L
K
A
10
Chain 3
1
L
V
F
F
A
A
X
L
K
A
10
Chain 4
1
L
V
F
F
A
A
X
L
K
A
10
Chain 5
1
L
V
F
F
A
A
X
L
K
A
10
Chain 6
1
L
V
F
F
A
A
X
L
K
A
10
Chain 7
1
L
V
F
F
A
A
X
L
K
A
10
Chain 8
1
L
V
F
F
A
A
X
L
K
A
10
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
LVFFA segment from Alzheimer's Amyloid-Beta displayed on 42-membered macrocycle scaffold
They explore oligomer structure using a model system: macrocyclic peptides. Key amyloidogenic sequences from ABeta and tau were incorporated into macrocycles, thereby restraining them to Beta-strands, but limiting the growth of the oligomers so they may crystallize and cannot fibrillate. Oligomers reveal tetrameric interfaces in which Beta-sheet dimers pair together by highly complementary, dry interfaces, analogous to steric zippers found in fibers, suggesting a common structure for amyloid oligomers and fibers. In amyloid fibers, the axes of the paired sheets are either parallel or antiparallel, whereas the oligomeric interfaces display a variety of sheet-to-sheet pairing angles, offering a structural explanation for the heterogeneity of amyloid oligomers.
Literature
PMID:
21473620
Author(s):
Liu, C., Sawaya, M.R., Cheng, P.N., Zheng, J., Nowick, J.S., Eisenberg, D.
Reference:
J Am Chem Soc. 2011 May 4;133(17):6736-44.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Amyloid-Beta
Alternative Name:
Gene Name:
Sequence Length:
10
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Cyclic pseudo-peptide LVFFA(ORN)(HAO)LK(ORN)
Structure Information
PDB ID:
3Q9H
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.25
R free:
0.222
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
HAO
A
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
A
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
SO4
A
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
BU1
B
C4 H10 O2
90.12
1,4-BUTANEDIOL
C(CCO)CO
WERYXYBDKMZEQL-UHFFFAOYSA-N
GOL
B
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
HAO
B
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
B
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
BU1
C
C4 H10 O2
90.12
1,4-BUTANEDIOL
C(CCO)CO
WERYXYBDKMZEQL-UHFFFAOYSA-N
GOL
C
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
HAO
C
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
C
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
GOL
D
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
HAO
D
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
D
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
BU1
E
C4 H10 O2
90.12
1,4-BUTANEDIOL
C(CCO)CO
WERYXYBDKMZEQL-UHFFFAOYSA-N
HAO
E
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
E
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
SO4
E
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
BU1
F
C4 H10 O2
90.12
1,4-BUTANEDIOL
C(CCO)CO
WERYXYBDKMZEQL-UHFFFAOYSA-N
HAO
F
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
F
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
BU1
G
C4 H10 O2
90.12
1,4-BUTANEDIOL
C(CCO)CO
WERYXYBDKMZEQL-UHFFFAOYSA-N
HAO
G
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
G
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
SO4
G
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
BU1
H
C4 H10 O2
90.12
1,4-BUTANEDIOL
C(CCO)CO
WERYXYBDKMZEQL-UHFFFAOYSA-N
GOL
H
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
HAO
H
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
H
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
SO4
H
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
Entry:S-0295
PDB ID: 3Q9I
CSV
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
L
V
Y
F
A
A
X
L
K
A
10
Chain 2
1
L
V
Y
F
A
A
X
L
K
A
10
Chain 3
1
L
V
Y
F
A
A
X
L
K
A
10
Chain 4
1
L
V
Y
F
A
A
X
L
K
A
10
Chain 5
1
L
V
Y
F
A
A
X
L
K
A
10
Chain 6
1
L
V
Y
F
A
A
X
L
K
A
10
Chain 7
1
L
V
Y
F
A
A
X
L
K
A
10
Chain 8
1
L
V
Y
F
A
A
X
L
K
A
10
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
LVFFA segment from Alzheimer's Amyloid-Beta displayed on 42-membered macrocycle scaffold, bromide derivative
They explore oligomer structure using a model system: macrocyclic peptides. Key amyloidogenic sequences from ABeta and tau were incorporated into macrocycles, thereby restraining them to Beta-strands, but limiting the growth of the oligomers so they may crystallize and cannot fibrillate. Oligomers reveal tetrameric interfaces in which Beta-sheet dimers pair together by highly complementary, dry interfaces, analogous to steric zippers found in fibers, suggesting a common structure for amyloid oligomers and fibers. In amyloid fibers, the axes of the paired sheets are either parallel or antiparallel, whereas the oligomeric interfaces display a variety of sheet-to-sheet pairing angles, offering a structural explanation for the heterogeneity of amyloid oligomers.
Literature
PMID:
21473620
Author(s):
Liu, C., Sawaya, M.R., Cheng, P.N., Zheng, J., Nowick, J.S., Eisenberg, D.
Reference:
J Am Chem Soc. 2011 May 4;133(17):6736-44.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Amyloid-Beta
Alternative Name:
Gene Name:
Sequence Length:
10
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
Structure Information
PDB ID:
3Q9I
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.99
R free:
0.218
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
4BF
A
C9 H10 Br N O2
244.09
4-BROMO-L-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)Br
PEMUHKUIQHFMTH-QMMMGPOBSA-N
CL
A
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
HAO
A
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
A
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
4BF
B
C9 H10 Br N O2
244.09
4-BROMO-L-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)Br
PEMUHKUIQHFMTH-QMMMGPOBSA-N
GOL
B
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
HAO
B
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
B
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
4BF
C
C9 H10 Br N O2
244.09
4-BROMO-L-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)Br
PEMUHKUIQHFMTH-QMMMGPOBSA-N
GOL
C
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
HAO
C
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
C
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
4BF
D
C9 H10 Br N O2
244.09
4-BROMO-L-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)Br
PEMUHKUIQHFMTH-QMMMGPOBSA-N
CL
D
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL
D
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
HAO
D
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
D
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
4BF
E
C9 H10 Br N O2
244.09
4-BROMO-L-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)Br
PEMUHKUIQHFMTH-QMMMGPOBSA-N
CL
E
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
HAO
E
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
IPA
E
C3 H8 O
60.1
ISOPROPYL ALCOHOL
CC(C)O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
ORN
E
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
4BF
F
C9 H10 Br N O2
244.09
4-BROMO-L-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)Br
PEMUHKUIQHFMTH-QMMMGPOBSA-N
HAO
F
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
F
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
4BF
G
C9 H10 Br N O2
244.09
4-BROMO-L-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)Br
PEMUHKUIQHFMTH-QMMMGPOBSA-N
HAO
G
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
G
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
4BF
H
C9 H10 Br N O2
244.09
4-BROMO-L-PHENYLALANINE
c1cc(ccc1C[C@@H](C(=O)O)N)Br
PEMUHKUIQHFMTH-QMMMGPOBSA-N
CL
H
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
HAO
H
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
IPA
H
C3 H8 O
60.1
ISOPROPYL ALCOHOL
CC(C)O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
ORN
H
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
Entry:S-0296
PDB ID: 3Q9J
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
A
I
I
F
L
A
X
Y
K
A
10
Chain 2
1
A
I
I
F
L
A
X
Y
K
A
10
Chain 3
1
A
I
I
F
L
A
X
Y
K
A
10
Chain 4
1
A
I
I
F
L
A
X
Y
K
A
10
Chain 5
1
A
I
I
F
L
A
X
Y
K
A
10
Chain 6
1
A
I
I
F
L
A
X
Y
K
A
10
Chain 7
1
A
I
I
F
L
A
X
Y
K
A
10
Chain 8
1
A
I
I
F
L
A
X
Y
K
A
10
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
AIIFL segment derived from Alzheimer's Amyloid-Beta displayed on 42-membered macrocycle scaffold
They explore oligomer structure using a model system: macrocyclic peptides. Key amyloidogenic sequences from ABeta and tau were incorporated into macrocycles, thereby restraining them to Beta-strands, but limiting the growth of the oligomers so they may crystallize and cannot fibrillate. Oligomers reveal tetrameric interfaces in which Beta-sheet dimers pair together by highly complementary, dry interfaces, analogous to steric zippers found in fibers, suggesting a common structure for amyloid oligomers and fibers. In amyloid fibers, the axes of the paired sheets are either parallel or antiparallel, whereas the oligomeric interfaces display a variety of sheet-to-sheet pairing angles, offering a structural explanation for the heterogeneity of amyloid oligomers.
Literature
PMID:
21473620
Author(s):
Liu, C., Sawaya, M.R., Cheng, P.N., Zheng, J., Nowick, J.S., Eisenberg, D.
Reference:
J Am Chem Soc. 2011 May 4;133(17):6736-44.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Amyloid-Beta
Alternative Name:
Gene Name:
Sequence Length:
10
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
Structure Information
PDB ID:
3Q9J
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.55
R free:
0.223
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
HAO
A
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
A
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
ZN
A
Zn 2
65.41
ZINC ION
[Zn+2]
PTFCDOFLOPIGGS-UHFFFAOYSA-N
GOL
B
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
HAO
B
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
B
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
ZN
B
Zn 2
65.41
ZINC ION
[Zn+2]
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
C
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
HAO
C
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
C
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
CL
D
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
HAO
D
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
D
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
CL
E
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
HAO
E
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
E
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
ZN
E
Zn 2
65.41
ZINC ION
[Zn+2]
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
F
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
HAO
F
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
F
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
ZN
F
Zn 2
65.41
ZINC ION
[Zn+2]
PTFCDOFLOPIGGS-UHFFFAOYSA-N
GOL
G
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
HAO
G
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
G
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
GOL
H
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
HAO
H
C10 H11 N3 O5
253.21
{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid
COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O
GRLLMVZTTMERGI-UHFFFAOYSA-N
ORN
H
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
Entry:S-0297
PDB ID: 3SGM
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
K
X
K
V
L
G
D
V
I
E
V
11
Chain 2
1
K
X
K
V
L
G
D
V
I
E
V
11
Chain 3
1
K
X
K
V
L
G
D
V
I
E
V
11
Chain 4
1
K
X
K
V
L
G
D
V
I
E
V
11
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Bromoderivative-2 of amyloid-related segment of alphaB-crystallin residues 90-100
They identify a segment of the amyloid-forming protein AlphaB crystallin, which forms an oligomeric complex exhibiting properties of other amyloid oligomers: Beta-sheet-rich structure, cytotoxicity, and recognition by an oligomer-specific antibody. The x-ray-derived atomic structure of the oligomer reveals a cylindrical barrel, formed from six antiparallel protein strands, that was termed cylindrin.
Literature
PMID:
22403391
Author(s):
Laganowsky, A., Liu, C., Sawaya, M.R., Whitelegge, J.P., Park, J., Zhao, M., Pensalfini, A., Soriaga, A.B., Landau, M., Teng, P.K., Cascio, D., Glabe, C., Eisenberg, D.
Reference:
Science. 2012 Mar 9;335(6073):1228-31.
Download
Entry:
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Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Alpha-crystallin B chain
Alternative Name:
Gene Name:
Sequence Length:
11
Species:
Homo sapiens
Mutation(s):
K11V-Br2
E.C. Number:
UniProt ID:
P02511
Keyword(s):
Alpha-crystallin B chain
Structure Information
PDB ID:
3SGM
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 6-mer - A6
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.7
R free:
0.24
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
A8E
A
C5 H8 Br N O2
194.03
(2S)-2-amino-4-bromopent-4-enoic acid
C=C(C[C@@H](C(=O)O)N)Br
YTCSGBSYHNQHFD-BYPYZUCNSA-N
A8E
B
C5 H8 Br N O2
194.03
(2S)-2-amino-4-bromopent-4-enoic acid
C=C(C[C@@H](C(=O)O)N)Br
YTCSGBSYHNQHFD-BYPYZUCNSA-N
MPD
B
C6 H14 O2
118.17
(4S)-2-METHYL-2,4-PENTANEDIOL
C[C@@H](CC(C)(C)O)O
SVTBMSDMJJWYQN-YFKPBYRVSA-N
A8E
C
C5 H8 Br N O2
194.03
(2S)-2-amino-4-bromopent-4-enoic acid
C=C(C[C@@H](C(=O)O)N)Br
YTCSGBSYHNQHFD-BYPYZUCNSA-N
A8E
D
C5 H8 Br N O2
194.03
(2S)-2-amino-4-bromopent-4-enoic acid
C=C(C[C@@H](C(=O)O)N)Br
YTCSGBSYHNQHFD-BYPYZUCNSA-N
Entry:S-0298
PDB ID: 3SGN
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
K
V
K
V
L
G
D
X
I
E
V
11
Chain 2
1
K
V
K
V
L
G
D
X
I
E
V
11
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Bromoderivative-8 of amyloid-related segment of alphaB-crystallin residues 90-100
They identify a segment of the amyloid-forming protein AlphaB crystallin, which forms an oligomeric complex exhibiting properties of other amyloid oligomers: Beta-sheet-rich structure, cytotoxicity, and recognition by an oligomer-specific antibody. The x-ray-derived atomic structure of the oligomer reveals a cylindrical barrel, formed from six antiparallel protein strands, that was termed cylindrin.
Literature
PMID:
22403391
Author(s):
Laganowsky, A., Liu, C., Sawaya, M.R., Whitelegge, J.P., Park, J., Zhao, M., Pensalfini, A., Soriaga, A.B., Landau, M., Teng, P.K., Cascio, D., Glabe, C., Eisenberg, D.
Reference:
Science. 2012 Mar 9;335(6073):1228-31.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Alpha-crystallin B chain
Alternative Name:
Gene Name:
Sequence Length:
11
Species:
Homo sapiens
Mutation(s):
K11V-Br8
E.C. Number:
UniProt ID:
P02511
Keyword(s):
Alpha-crystallin B chain
Structure Information
PDB ID:
3SGN
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 6-mer - A6
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.81
R free:
0.22699999
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
A8E
A
C5 H8 Br N O2
194.03
(2S)-2-amino-4-bromopent-4-enoic acid
C=C(C[C@@H](C(=O)O)N)Br
YTCSGBSYHNQHFD-BYPYZUCNSA-N
A8E
B
C5 H8 Br N O2
194.03
(2S)-2-amino-4-bromopent-4-enoic acid
C=C(C[C@@H](C(=O)O)N)Br
YTCSGBSYHNQHFD-BYPYZUCNSA-N
Entry:S-0299
PDB ID: 3SGO
CSV
JSON
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
K
V
K
V
L
G
D
V
I
E
V
11
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Amyloid-related segment of alphaB-crystallin residues 90-100
They identify a segment of the amyloid-forming protein AlphaB crystallin, which forms an oligomeric complex exhibiting properties of other amyloid oligomers: Beta-sheet-rich structure, cytotoxicity, and recognition by an oligomer-specific antibody. The x-ray-derived atomic structure of the oligomer reveals a cylindrical barrel, formed from six antiparallel protein strands, that was termed cylindrin.
Literature
PMID:
22403391
Author(s):
Laganowsky, A., Liu, C., Sawaya, M.R., Whitelegge, J.P., Park, J., Zhao, M., Pensalfini, A., Soriaga, A.B., Landau, M., Teng, P.K., Cascio, D., Glabe, C., Eisenberg, D.
Reference:
Science. 2012 Mar 9;335(6073):1228-31.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Alpha-crystallin B chain
Alternative Name:
Gene Name:
Sequence Length:
11
Species:
Homo sapiens
Mutation(s):
K11V
E.C. Number:
UniProt ID:
P02511
Keyword(s):
Alpha-crystallin B chain
Structure Information
PDB ID:
3SGO
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 6-mer - A6
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.56
R free:
0.27
Entry:S-0300
PDB ID: 3SGP
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
K
L
K
V
L
G
D
V
I
E
V
11
Chain 2
1
K
L
K
V
L
G
D
V
I
E
V
11
Chain 3
1
K
L
K
V
L
G
D
V
I
E
V
11
Chain 4
1
K
L
K
V
L
G
D
V
I
E
V
11
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Amyloid-related segment of alphaB-crystallin residues 90-100 mutant V91L
They identify a segment of the amyloid-forming protein AlphaB crystallin, which forms an oligomeric complex exhibiting properties of other amyloid oligomers: Beta-sheet-rich structure, cytotoxicity, and recognition by an oligomer-specific antibody. The x-ray-derived atomic structure of the oligomer reveals a cylindrical barrel, formed from six antiparallel protein strands, that was termed cylindrin.
Literature
PMID:
22403391
Author(s):
Laganowsky, A., Liu, C., Sawaya, M.R., Whitelegge, J.P., Park, J., Zhao, M., Pensalfini, A., Soriaga, A.B., Landau, M., Teng, P.K., Cascio, D., Glabe, C., Eisenberg, D.
Reference:
Science. 2012 Mar 9;335(6073):1228-31.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Alpha-crystallin B chain
Alternative Name:
Gene Name:
Sequence Length:
11
Species:
Homo sapiens
Mutation(s):
K11V, V2L
E.C. Number:
UniProt ID:
P02511
Keyword(s):
Alpha-crystallin B chain
Structure Information
PDB ID:
3SGP
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 6-mer - A6
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.4
R free:
0.23800000
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
MRD
A
C6 H14 O2
118.17
(4R)-2-METHYLPENTANE-2,4-DIOL
C[C@H](CC(C)(C)O)O
SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD
B
C6 H14 O2
118.17
(4S)-2-METHYL-2,4-PENTANEDIOL
C[C@@H](CC(C)(C)O)O
SVTBMSDMJJWYQN-YFKPBYRVSA-N
MPD
C
C6 H14 O2
118.17
(4S)-2-METHYL-2,4-PENTANEDIOL
C[C@@H](CC(C)(C)O)O
SVTBMSDMJJWYQN-YFKPBYRVSA-N
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