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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
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Peptide Sequence
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PDB ID
Method
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Displaying 31 to 60 records out of 565 records fetched.
Entry
PDB ID
Protein
Name
Species
Length
Mutation(s)
Class
Type
Method
Resolution (
Å
)
PMID
S-0031
1GYK
Serum amyloid P-component
Homo sapiens
204
No
Amyloid
Protein complex
X-RAY DIFFRACTION
2.2
12126626
S-0032
1HZ3
Amyloid-beta A4 protein
Homo sapiens
26
No
Amyloid
Peptide
SOLUTION NMR
10940221
S-0033
1III
Transthyretin
Homo sapiens
127
Y114C
Amyloid
Protein
X-RAY DIFFRACTION
2.0
12403615
S-0034
1IIK
Transthyretin
Homo sapiens
127
Y114C
Non-amyloid
Protein
X-RAY DIFFRACTION
2.0
12403615
S-0035
1IJN
Transthyretin
Homo sapiens
127
C10A/Y114C
Amyloid
Protein
X-RAY DIFFRACTION
1.7
16185074
S-0036
1IOC
Lysozyme C
Homo sapiens
134
EAEA (insert at N-terminal)-I56T
Amyloid
Protein
X-RAY DIFFRACTION
2.4
12359083
S-0037
1IYT
Amyloid-beta A4 protein
Homo sapiens
42
No
Amyloid
Peptide
SOLUTION NMR
12423364
S-0038
1JNJ
Beta-2-microglobulin
Homo sapiens
100
No
Amyloid
Protein
SOLUTION NMR
11847272
S-0039
1JVK
Uncharacterized protein
Homo sapiens
216
No
Amyloid
Protein
X-RAY DIFFRACTION
1.94
11976493
S-0040
1KUW
Islet amyloid polypeptide
Homo sapiens
10
No
Amyloid
Peptide
SOLUTION NMR
12717720
S-0041
1LGN
Serum amyloid P-component
Homo sapiens
204
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
2.8
9217261
S-0042
1LOZ
Lysozyme C
Homo sapiens
130
I56T
Amyloid
Protein
X-RAY DIFFRACTION
1.8
9039909
S-0043
1LYY
Lysozyme C
Homo sapiens
130
D67H
Amyloid
Protein
X-RAY DIFFRACTION
1.8
9039909
S-0044
1N9J
Cystatin-A
Homo sapiens
98
No
Amyloid
Protein
SOLUTION NMR
11532941
S-0045
1NMJ
Amyloid-beta A4 protein
Rattus norvegicus
28
No
Non-amyloid
Peptide
SOLUTION NMR
15160315
S-0046
1OEZ
Superoxide dismutase [Cu-Zn]
Homo sapiens
153
Zn-H46R
Amyloid
Protein
X-RAY DIFFRACTION
2.15
12754496
S-0047
1OP9
lysozyme
121 , 130
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
1.86
12917687
S-0048
1OUA
Lysozyme C
Homo sapiens
130
I56T
Amyloid
Protein
X-RAY DIFFRACTION
1.8
9010773
S-0049
1OZT
Superoxide dismutase [Cu-Zn]
Homo sapiens
153
apo-H46R
Amyloid
Protein
X-RAY DIFFRACTION
2.5
12754496
S-0050
1OZU
Superoxide dismutase [Cu-Zn]
Homo sapiens
153
S134N
Amyloid
Protein
X-RAY DIFFRACTION
1.3
12754496
S-0051
1PY4
Beta-2-microglobulin
Homo sapiens
100
H31Y
Amyloid
Protein
X-RAY DIFFRACTION
2.9
14698299
S-0052
1Q38
Fibronectin
Homo sapiens
89
No
Amyloid
Protein
SOLUTION NMR
12946358
S-0053
1QCM
Amyloid-beta A4 protein
Homo sapiens
11
No
Amyloid
Peptide
SOLUTION NMR
8973180
S-0054
1QJH
30S ribosomal protein S6
Thermus thermophilus
101
E41A/E42I/R46M/R47V
Amyloid
Protein
X-RAY DIFFRACTION
2.2
10944185
S-0055
1QP1
Immunoglobulin kappa variable 1-33
Homo sapiens
107
No
Amyloid
Protein
X-RAY DIFFRACTION
2.06
9990143
S-0056
1QWP
Amyloid-beta A4 protein
Homo sapiens
11
No
Amyloid
Peptide
SOLUTION NMR
15293994
S-0057
1QXC
Amyloid-beta A4 protein
Homo sapiens
11
No
Amyloid
Peptide
SOLUTION NMR
15293994
S-0058
1QYT
Amyloid-beta A4 protein
Homo sapiens
11
No
Amyloid
Peptide
SOLUTION NMR
15293994
S-0059
1R4C
Cystatin-C
Homo sapiens
110
L68Q, 10 residue truncated fron N-terminal
Amyloid
Protein
X-RAY DIFFRACTION
2.18
15312769
S-0060
1RVS
Transthyretin
Rattus norvegicus
11
No
Amyloid
FIbril
SOLID-STATE NMR
14715898
Entry:S-0031
PDB ID: 1GYK
CSV
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
H
T
D
L
S
G
K
V
F
V
F
P
R
E
S
V
T
D
H
V
N
L
I
T
P
25
26
L
E
K
P
L
Q
N
F
T
L
C
F
R
A
Y
S
D
L
S
R
A
Y
S
L
F
50
51
S
Y
N
T
Q
G
R
D
N
E
L
L
V
Y
K
E
R
V
G
E
Y
S
L
Y
I
75
76
G
R
H
K
V
T
S
K
V
I
E
K
F
P
A
P
V
H
I
C
V
S
W
E
S
100
101
S
S
G
I
A
E
F
W
I
N
G
T
P
L
V
K
K
G
L
R
Q
G
Y
F
V
125
126
E
A
Q
P
K
I
V
L
G
Q
E
Q
D
S
Y
G
G
K
F
D
R
S
Q
S
F
150
151
V
G
E
I
G
D
L
Y
M
W
D
S
V
L
P
P
E
N
I
L
S
A
Y
Q
G
175
176
T
P
L
P
A
N
I
L
D
W
Q
A
L
N
Y
E
I
R
G
Y
V
I
I
K
P
200
201
L
V
W
V
204
Chain 2
1
H
T
D
L
S
G
K
V
F
V
F
P
R
E
S
V
T
D
H
V
N
L
I
T
P
25
26
L
E
K
P
L
Q
N
F
T
L
C
F
R
A
Y
S
D
L
S
R
A
Y
S
L
F
50
51
S
Y
N
T
Q
G
R
D
N
E
L
L
V
Y
K
E
R
V
G
E
Y
S
L
Y
I
75
76
G
R
H
K
V
T
S
K
V
I
E
K
F
P
A
P
V
H
I
C
V
S
W
E
S
100
101
S
S
G
I
A
E
F
W
I
N
G
T
P
L
V
K
K
G
L
R
Q
G
Y
F
V
125
126
E
A
Q
P
K
I
V
L
G
Q
E
Q
D
S
Y
G
G
K
F
D
R
S
Q
S
F
150
151
V
G
E
I
G
D
L
Y
M
W
D
S
V
L
P
P
E
N
I
L
S
A
Y
Q
G
175
176
T
P
L
P
A
N
I
L
D
W
Q
A
L
N
Y
E
I
R
G
Y
V
I
I
K
P
200
201
L
V
W
V
204
Chain 3
1
H
T
D
L
S
G
K
V
F
V
F
P
R
E
S
V
T
D
H
V
N
L
I
T
P
25
26
L
E
K
P
L
Q
N
F
T
L
C
F
R
A
Y
S
D
L
S
R
A
Y
S
L
F
50
51
S
Y
N
T
Q
G
R
D
N
E
L
L
V
Y
K
E
R
V
G
E
Y
S
L
Y
I
75
76
G
R
H
K
V
T
S
K
V
I
E
K
F
P
A
P
V
H
I
C
V
S
W
E
S
100
101
S
S
G
I
A
E
F
W
I
N
G
T
P
L
V
K
K
G
L
R
Q
G
Y
F
V
125
126
E
A
Q
P
K
I
V
L
G
Q
E
Q
D
S
Y
G
G
K
F
D
R
S
Q
S
F
150
151
V
G
E
I
G
D
L
Y
M
W
D
S
V
L
P
P
E
N
I
L
S
A
Y
Q
G
175
176
T
P
L
P
A
N
I
L
D
W
Q
A
L
N
Y
E
I
R
G
Y
V
I
I
K
P
200
201
L
V
W
V
204
Chain 4
1
H
T
D
L
S
G
K
V
F
V
F
P
R
E
S
V
T
D
H
V
N
L
I
T
P
25
26
L
E
K
P
L
Q
N
F
T
L
C
F
R
A
Y
S
D
L
S
R
A
Y
S
L
F
50
51
S
Y
N
T
Q
G
R
D
N
E
L
L
V
Y
K
E
R
V
G
E
Y
S
L
Y
I
75
76
G
R
H
K
V
T
S
K
V
I
E
K
F
P
A
P
V
H
I
C
V
S
W
E
S
100
101
S
S
G
I
A
E
F
W
I
N
G
T
P
L
V
K
K
G
L
R
Q
G
Y
F
V
125
126
E
A
Q
P
K
I
V
L
G
Q
E
Q
D
S
Y
G
G
K
F
D
R
S
Q
S
F
150
151
V
G
E
I
G
D
L
Y
M
W
D
S
V
L
P
P
E
N
I
L
S
A
Y
Q
G
175
176
T
P
L
P
A
N
I
L
D
W
Q
A
L
N
Y
E
I
R
G
Y
V
I
I
K
P
200
201
L
V
W
V
204
Chain 5
1
H
T
D
L
S
G
K
V
F
V
F
P
R
E
S
V
T
D
H
V
N
L
I
T
P
25
26
L
E
K
P
L
Q
N
F
T
L
C
F
R
A
Y
S
D
L
S
R
A
Y
S
L
F
50
51
S
Y
N
T
Q
G
R
D
N
E
L
L
V
Y
K
E
R
V
G
E
Y
S
L
Y
I
75
76
G
R
H
K
V
T
S
K
V
I
E
K
F
P
A
P
V
H
I
C
V
S
W
E
S
100
101
S
S
G
I
A
E
F
W
I
N
G
T
P
L
V
K
K
G
L
R
Q
G
Y
F
V
125
126
E
A
Q
P
K
I
V
L
G
Q
E
Q
D
S
Y
G
G
K
F
D
R
S
Q
S
F
150
151
V
G
E
I
G
D
L
Y
M
W
D
S
V
L
P
P
E
N
I
L
S
A
Y
Q
G
175
176
T
P
L
P
A
N
I
L
D
W
Q
A
L
N
Y
E
I
R
G
Y
V
I
I
K
P
200
201
L
V
W
V
204
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
The Structures of Crystalline Complexes of Human Serum Amyloid P Component with its Carbohydrate Ligand
The ability of MObDG (ligand) to displace SAP from amyloid fibres in-vitro suggests that the calcium binding site is involved in amyloid recognition and furthermore that this small compound mimics elements of the pathological substrate. The working hypothesis is that b-turns linking strands of the crossed-b structure of the fibre are good candidates for the recognition motif. It is notable that the array of interactions between MObDG andSAP can broadly mimic a tight b-turn carrying aspartic acid at the apex. Although such motifs are common in amyloid precursor proteins they are not universally present.
Literature
PMID:
12126626
Author(s):
Thompson, D., Pepys, M.B., Tickle, I., Wood, S.P.
Reference:
J Mol Biol. 2002 Jul 26;320(5):1081-6
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Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Serum amyloid P-component
Alternative Name:
9.5S alpha-1-glycoprotein
Gene Name:
APCS, PTX2
Sequence Length:
204
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P02743
Keyword(s):
SERUM AMYLOID P-COMPONENT
Structure Information
PDB ID:
1GYK
Amyloid Category:
Amyloid
Type:
Protein complex
Global Stoichiometry:
Homo 5-mer - A5
PDB Classification:
GLYCOPROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.2
R free:
0.22399999
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
CA
A
Ca 2
40.08
CALCIUM ION
[Ca+2]
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CDG
A
C10 H16 O8
264.23
METHYL 4,6-O-[(1R)-1-CARBOXYETHYLIDENE]-BETA-D-GALACTOPYRANOSIDE
C[C@]1(OC[C@@H]2[C@H](O1)[C@@H]([C@H]([C@@H](O2)OC)O)O)C(=O)O
ZDZVLEQWFATHTF-IJWOWSJNSA-N
CA
B
Ca 2
40.08
CALCIUM ION
[Ca+2]
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CDG
B
C10 H16 O8
264.23
METHYL 4,6-O-[(1R)-1-CARBOXYETHYLIDENE]-BETA-D-GALACTOPYRANOSIDE
C[C@]1(OC[C@@H]2[C@H](O1)[C@@H]([C@H]([C@@H](O2)OC)O)O)C(=O)O
ZDZVLEQWFATHTF-IJWOWSJNSA-N
CA
C
Ca 2
40.08
CALCIUM ION
[Ca+2]
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CDG
C
C10 H16 O8
264.23
METHYL 4,6-O-[(1R)-1-CARBOXYETHYLIDENE]-BETA-D-GALACTOPYRANOSIDE
C[C@]1(OC[C@@H]2[C@H](O1)[C@@H]([C@H]([C@@H](O2)OC)O)O)C(=O)O
ZDZVLEQWFATHTF-IJWOWSJNSA-N
CA
D
Ca 2
40.08
CALCIUM ION
[Ca+2]
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CDG
D
C10 H16 O8
264.23
METHYL 4,6-O-[(1R)-1-CARBOXYETHYLIDENE]-BETA-D-GALACTOPYRANOSIDE
C[C@]1(OC[C@@H]2[C@H](O1)[C@@H]([C@H]([C@@H](O2)OC)O)O)C(=O)O
ZDZVLEQWFATHTF-IJWOWSJNSA-N
CA
E
Ca 2
40.08
CALCIUM ION
[Ca+2]
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Entry:S-0032
PDB ID: 1HZ3
CSV
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Structure
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Sequence & Sec. Str.
Chain 1
1
Y
E
V
H
H
Q
K
L
V
F
F
A
E
D
V
G
S
N
K
G
A
I
I
G
L
25
26
M
26
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
The Alzheimer's peptide a beta adopts a collapsed coil structure in water
In contrast to studies in other solvents, in water ABeta is collapsed into a compact series of loops, strands, and turns and has no Alpha-helical or Beta-sheet structure. Conformational stabilization is primarily attributed to van der Waals and electrostatic forces. A large conspicuous uninterrupted hydrophobic patch covers approximately 25% of the surface. The compact coil structure appears meta-stable, and because fibrillization leads to formation of intermolecular Beta-sheet secondary structure, a global conformational rearrangement is highly likely.
Literature
PMID:
10940221
Author(s):
Zhang, S., Iwata, K., Lachenmann, M.J., Peng, J.W., Li, S., Stimson, E.R., Lu, Y., Felix, A.M., Maggio, J.E., Lee, J.P.
Reference:
J Struct Biol. 2000 Jun;130(2-3):130-41
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
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JSON
Protein Information
Protein Name:
Amyloid-beta A4 protein
Alternative Name:
ABPP, APPI, Alzheimer disease amyloid protein, Amyloid precursor protein, Amyloid-beta precursor protein, Cerebral vascular amyloid peptide, PreA4, Protease nexin-II
Gene Name:
APP, A4, AD1
Sequence Length:
26
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P05067
Keyword(s):
A-BETA AMYLOID
Structure Information
PDB ID:
1HZ3
Amyloid Category:
Amyloid
Type:
Peptide
Global Stoichiometry:
Monomer - A
PDB Classification:
SUGAR BINDING PROTEIN
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Entry:S-0033
PDB ID: 1III
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
C
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 2
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
C
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Disulfide-Bond Formation in the Transthyretin Mutant Y114C Prevents Amyloid Fibril Formation, Room temperature
Crystal structure of the transthyretin mutant TTR Y114C-data collected at room temperature.The Y114C mutation in human transthyretin (TTR) is associated with a particular form of familial amyloidotic polyneuropathy. In vitro ATTR Y114C mutant exists in three forms: one unstable but native like tetrameric form, one highly aggregated form in which a network of disulfide bonds is formed, and one fibrillar form. The disulfide-linked aggregates and the fibrillar form of the mutant can be induced by heat induction under nonreduced and reduced conditions, respectively. Both forms are recognized by the amyloid specific antibody MAB(39-44). ATTR Y114C mutant associates into normal tetramers, but starts forming aggregates at ?37 °C.
Literature
PMID:
12403615
Author(s):
Eneqvist, T., Olofsson, A., Ando, Y., Miyakawa, T., Katsuragi, S., Jass, J., Lundgren, E., Sauer-Eriksson, A.E.
Reference:
Biochemistry. 2002 Nov 5;41(44):13143-51
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Entry:
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Structure:
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FASTA
Contact Network:
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Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
127
Species:
Homo sapiens
Mutation(s):
Y114C
E.C. Number:
UniProt ID:
P02766
Keyword(s):
TRANSTHYRETIN
Structure Information
PDB ID:
1III
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
TRANSPORT PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.0
R free:
0.235
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
BME
A
C2 H6 O S
78.13
BETA-MERCAPTOETHANOL
C(CS)O
DGVVWUTYPXICAM-UHFFFAOYSA-N
BME
B
C2 H6 O S
78.13
BETA-MERCAPTOETHANOL
C(CS)O
DGVVWUTYPXICAM-UHFFFAOYSA-N
Entry:S-0034
PDB ID: 1IIK
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
C
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 2
1
G
P
T
G
T
G
E
S
K
C
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
C
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Disulfide-Bond Formation in the Transthyretin Mutant Y114C Prevents Amyloid Fibril Formation, CRYO temperature
Crystal structure of the transthyretin mutant TTR Y114C-data collected at cryo temperature. The Y114C mutation in human transthyretin (TTR) is associated with a particular form of familial amyloidotic polyneuropathy. In vitro ATTR Y114C mutant exists in three forms: one unstable but native like tetrameric form, one highly aggregated form in which a network of disulfide bonds is formed, and one fibrillar form. The disulfide-linked aggregates and the fibrillar form of the mutant can be induced by heat induction under nonreduced and reduced conditions, respectively. Both forms are recognized by the amyloid specific antibody MAB(39-44). ATTR Y114C mutant associates into normal tetramers, but starts forming aggregates at ?37 °C.
Literature
PMID:
12403615
Author(s):
Eneqvist, T., Olofsson, A., Ando, Y., Miyakawa, T., Katsuragi, S., Jass, J., Lundgren, E., Sauer-Eriksson, A.E.
Reference:
Biochemistry. 2002 Nov 5;41(44):13143-51
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Entry:
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Structure:
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FASTA
Contact Network:
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Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
127
Species:
Homo sapiens
Mutation(s):
Y114C
E.C. Number:
UniProt ID:
P02766
Keyword(s):
TRANSTHYRETIN
Structure Information
PDB ID:
1IIK
Amyloid Category:
Non-amyloid
Type:
Protein
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
TRANSPORT PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.0
R free:
0.239
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
BME
A
C2 H6 O S
78.13
BETA-MERCAPTOETHANOL
C(CS)O
DGVVWUTYPXICAM-UHFFFAOYSA-N
BME
B
C2 H6 O S
78.13
BETA-MERCAPTOETHANOL
C(CS)O
DGVVWUTYPXICAM-UHFFFAOYSA-N
Entry:S-0035
PDB ID: 1IJN
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
P
T
G
T
G
E
S
K
A
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
C
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Chain 2
1
G
P
T
G
T
G
E
S
K
A
P
L
M
V
K
V
L
D
A
V
R
G
S
P
A
25
26
I
N
V
A
V
H
V
F
R
K
A
A
D
D
T
W
E
P
F
A
S
G
K
T
S
50
51
E
S
G
E
L
H
G
L
T
T
E
E
E
F
V
E
G
I
Y
K
V
E
I
D
T
75
76
K
S
Y
W
K
A
L
G
I
S
P
F
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
L
L
S
P
C
S
Y
S
T
T
A
V
V
T
N
P
125
126
K
E
127
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Cys114-linked dimers of transthyretin are compatible with amyloid formation
TTR Cys10Ala/Tyr114Cys double mutant was generated and characterized to deduce the role of intermolecular disulfide bridging in fibril formation. The results suggest that an intermolecular cysteine bridge at position 114 enhances the exposure of cysteine 10, thereby facilitating additional intermolecular cysteine assemblies. This dimeric molecule can form protofibrils indistinguishable from the fibrils formed under reducing conditions.
Literature
PMID:
16185074
Author(s):
Karlsson, A., Olofsson, A., Eneqvist, T., Sauer-Eriksson, A.E.
Reference:
Biochemistry. 2005 Oct 4;44(39):13063-70
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Structure:
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Contact Network:
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Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
127
Species:
Homo sapiens
Mutation(s):
C10A/Y114C
E.C. Number:
UniProt ID:
P02766
Keyword(s):
TRANSTHYRETIN
Structure Information
PDB ID:
1IJN
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
TRANSPORT PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.7
R free:
0.237
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
BME
A
C2 H6 O S
78.13
BETA-MERCAPTOETHANOL
C(CS)O
DGVVWUTYPXICAM-UHFFFAOYSA-N
BME
B
C2 H6 O S
78.13
BETA-MERCAPTOETHANOL
C(CS)O
DGVVWUTYPXICAM-UHFFFAOYSA-N
Entry:S-0036
PDB ID: 1IOC
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
E
A
E
A
K
V
F
E
R
C
E
L
A
R
T
L
K
R
L
G
M
D
G
Y
R
25
26
G
I
S
L
A
N
W
M
C
L
A
K
W
E
S
G
Y
N
T
R
A
T
N
Y
N
50
51
A
G
D
R
S
T
D
Y
G
T
F
Q
I
N
S
R
Y
W
C
N
D
G
K
T
P
75
76
G
A
V
N
A
C
H
L
S
C
S
A
L
L
Q
D
N
I
A
D
A
V
A
C
A
100
101
K
R
V
V
R
D
P
Q
G
I
R
A
W
V
A
W
R
N
R
C
Q
N
R
D
V
125
126
R
Q
Y
V
Q
G
C
G
V
134
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Elongation in a beta-Structure Promotes Amyloid-Like Fibril Formation of Human Lysozyme
human lysozymes proteins: wild-type; I56T (amyloidogenic); EAEA (which has four additional residues Glu-Ala-Glu-Ala-) at the N-terminus located on a Beta-structure; and EAEA-I56T, which is an I56T mutant of EAEA. All formed amyloid-like fibrils through an in the increase contents of Alpha-helix with increasing concentration of ethanol. The order of propensity for amyloid-like fibril formation in highly concentrated ethanol solution is EAEA-I56T > EAEA > I56T > wild-type. This order is almost the reverse of the order of conformational stability of these proteins, wild-type > EAEA > I56T > EAEA-I56T.
Literature
PMID:
12359083
Author(s):
Goda, S., Takano, K., Yamagata, Y., Maki, S., Namba, K., Yutani, K.
Reference:
J Biochem. 2002 Oct;132(4):655-61
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Protein Information
Protein Name:
Lysozyme C
Alternative Name:
1, 4-beta-N-acetylmuramidase C
Gene Name:
LYZ, LZM
Sequence Length:
134
Species:
Homo sapiens
Mutation(s):
EAEA (insert at N-terminal)-I56T
E.C. Number:
3.2.1.17
UniProt ID:
P61626
Keyword(s):
LYSOZYME C
Structure Information
PDB ID:
1IOC
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
HYDROLASE
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.4
R free:
Entry:S-0037
PDB ID: 1IYT
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Sequence & Sec. Str.
Chain 1
1
D
A
E
F
R
H
D
S
G
Y
E
V
H
H
Q
K
L
V
F
F
A
E
D
V
G
25
26
S
N
K
G
A
I
I
G
L
M
V
G
G
V
V
I
A
42
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Solution structure of the Alzheimer's disease amyloid beta-peptide (1-42)
Exhaustive solvent scan performed showed a high propensity of ABeta-(1-42) to adopt helical conformations in aqueous solutions of fluorinated alcohols. The 3D NMR structure of ABeta-(1-42) shows two helical regions encompassing residues 8-25 and 28-38, connected by a regular type I Beta-turn. The surprising similarity of this structure, as well as the sequence of the C-terminal moiety, with those of the fusion domain of influenza hemagglutinin suggests a direct mechanism of neurotoxicity.
Literature
PMID:
12423364
Author(s):
Crescenzi, O., Tomaselli, S., Guerrini, R., Salvadori, S., D'Ursi, A.M., Temussi, P.A., Picone, D.
Reference:
Eur J Biochem. 2002 Nov;269(22):5642-8
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Protein Information
Protein Name:
Amyloid-beta A4 protein
Alternative Name:
ABPP, APPI, Alzheimer disease amyloid protein, Amyloid precursor protein, Amyloid-beta precursor protein, Cerebral vascular amyloid peptide, PreA4, Protease nexin-II
Gene Name:
APP, A4, AD1
Sequence Length:
42
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P05067
Keyword(s):
Alzheimer's disease amyloid
Structure Information
PDB ID:
1IYT
Amyloid Category:
Amyloid
Type:
Peptide
Global Stoichiometry:
Monomer - A
PDB Classification:
PROTEIN BINDING
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Entry:S-0038
PDB ID: 1JNJ
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Sequence & Sec. Str.
Chain 1
1
M
I
Q
R
T
P
K
I
Q
V
Y
S
R
H
P
A
E
N
G
K
S
N
F
L
N
25
26
C
Y
V
S
G
F
H
P
S
D
I
E
V
D
L
L
K
N
G
E
R
I
E
K
V
50
51
E
H
S
D
L
S
F
S
K
D
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
D
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
The solution structure of human beta2-microglobulin reveals the prodromes of its amyloid transition
Compared to previous structural data obtained from the NMR secondary structure of the isolated protein and the crystal structure of MHC-I, in which the protein is associated to the heavy-chain component, several differences are observed. The most important rearrangements were observed for (1) strands V and VI (loss of the C-terminal and N-terminal end, respectively), (2) interstrand loop V-VI, and (3) strand I, including the N-terminal segment (displacement outward of the molecular core). These modifications can be considered as the prodromes of the amyloid transition. Solvation of the protected regions in MHC-I decreases the tertiary packing by breaking the contiguity of the surface hydrophobic patches at the interface with heavy chain and the nearby region at the surface charge cluster of the C-terminal segment.
Literature
PMID:
11847272
Author(s):
Verdone, G., Corazza, A., Viglino, P., Pettirossi, F., Giorgetti, S., Mangione, P., Andreola, A., Stoppini, M., Bellotti, V., Esposito, G.
Reference:
Protein Sci. 2002 Mar;11(3):487-99
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Protein Information
Protein Name:
Beta-2-microglobulin
Alternative Name:
Gene Name:
B2M, CDABP0092, HDCMA22P
Sequence Length:
100
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P61769
Keyword(s):
beta2-microglobulin
Structure Information
PDB ID:
1JNJ
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
IMMUNE SYSTEM
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Entry:S-0039
PDB ID: 1JVK
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Sequence & Sec. Str.
Chain 1
1
E
T
A
L
T
Q
P
A
S
V
S
G
S
P
G
Q
S
I
T
V
S
C
T
G
V
25
26
S
S
I
V
G
S
Y
N
L
V
S
W
Y
Q
Q
H
P
G
K
A
P
K
L
L
T
50
51
Y
E
V
N
K
R
P
S
G
V
S
D
R
F
S
G
S
K
S
G
N
S
A
S
L
75
76
T
I
S
G
L
Q
A
E
D
E
A
D
Y
Y
C
S
S
Y
D
G
S
S
T
S
V
100
101
V
F
G
G
G
T
K
L
T
V
L
G
Q
P
K
A
A
P
S
V
T
L
F
P
P
125
126
S
S
E
E
L
Q
A
N
K
A
T
L
V
C
L
I
S
D
F
Y
P
G
A
V
T
150
151
V
A
W
K
A
D
S
S
P
V
K
A
G
V
E
T
T
K
P
S
K
Q
S
N
N
175
176
K
Y
A
A
S
S
Y
L
S
L
T
P
E
Q
W
K
S
H
R
S
Y
S
C
Q
V
200
201
T
H
E
G
S
T
V
E
K
T
V
A
P
T
A
C
216
Chain 2
1
E
T
A
L
T
Q
P
A
S
V
S
G
S
P
G
Q
S
I
T
V
S
C
T
G
V
25
26
S
S
I
V
G
S
Y
N
L
V
S
W
Y
Q
Q
H
P
G
K
A
P
K
L
L
T
50
51
Y
E
V
N
K
R
P
S
G
V
S
D
R
F
S
G
S
K
S
G
N
S
A
S
L
75
76
T
I
S
G
L
Q
A
E
D
E
A
D
Y
Y
C
S
S
Y
D
G
S
S
T
S
V
100
101
V
F
G
G
G
T
K
L
T
V
L
G
Q
P
K
A
A
P
S
V
T
L
F
P
P
125
126
S
S
E
E
L
Q
A
N
K
A
T
L
V
C
L
I
S
D
F
Y
P
G
A
V
T
150
151
V
A
W
K
A
D
S
S
P
V
K
A
G
V
E
T
T
K
P
S
K
Q
S
N
N
175
176
K
Y
A
A
S
S
Y
L
S
L
T
P
E
Q
W
K
S
H
R
S
Y
S
C
Q
V
200
201
T
H
E
G
S
T
V
E
K
T
V
A
P
T
A
C
216
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
THREE-DIMENSIONAL STRUCTURE OF AN IMMUNOGLOBULIN LIGHT CHAIN DIMER ACTING AS A LETHAL AMYLOID PRECURSOR
"The X-ray structure of an immunoglobulin light-chain dimer isolated from the urine as a ""Bence-Jones protein"" from a patient with multiple myeloma and amyloidosis (Sea). The urinary protein produced fibrillar amyloid deposits which were fatal to the patient. Compared with the amyloidogenic Mcg light-chain dimer, the Sea protein was highly soluble in aqueous solutions and only crystallized at concentrations approaching 100 mg ml(-1)."
Literature
PMID:
11976493
Author(s):
Bourne, P.C., Ramsland, P.A., Shan, L., Fan, Z.C., DeWitt, C.R., Shultz, B.B., Terzyan, S.S., Moomaw, C.R., Slaughter, C.A., Guddat, L.W., Edmundson, A.B.
Reference:
Acta Crystallogr D Biol Crystallogr. 2002 May;58(Pt 5):815-23. Epub 2002 Apr 26
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Entry:
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Structure:
PDB
CIF
FASTA
Contact Network:
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JSON
Protein Information
Protein Name:
Uncharacterized protein
Alternative Name:
Gene Name:
Sequence Length:
216
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Q6PJG0
Keyword(s):
IMMUNOGLOBULIN LAMBDA LIGHT CHAIN
Structure Information
PDB ID:
1JVK
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
IMMUNE SYSTEM
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.94
R free:
0.254
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
PCA
A
C5 H7 N O3
129.11
PYROGLUTAMIC ACID
C1CC(=O)N[C@@H]1C(=O)O
ODHCTXKNWHHXJC-VKHMYHEASA-N
PCA
B
C5 H7 N O3
129.11
PYROGLUTAMIC ACID
C1CC(=O)N[C@@H]1C(=O)O
ODHCTXKNWHHXJC-VKHMYHEASA-N
Entry:S-0040
PDB ID: 1KUW
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Structure
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Sequence & Sec. Str.
Chain 1
1
S
N
N
F
G
A
I
L
S
S
10
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Conformational preferences of the amylin nucleation site in SDS micelles
hIAPP constitutes approximately 90% of the amyloid deposits found in type II diabetic patients. It has been shown that the central region of the peptide (hIAPP(20-29)) constitutes the nucleation site for the amyloidogenic process with F23 playing a key role in the formation of the Beta-pleated structures.
Literature
PMID:
12717720
Author(s):
Mascioni, A., Porcelli, F., Ilangovan, U., Ramamoorthy, A., Veglia, G.
Reference:
Biopolymers. 2003 May;69(1):29-41
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Entry:
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Structure:
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FASTA
Contact Network:
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Protein Information
Protein Name:
Islet amyloid polypeptide
Alternative Name:
Gene Name:
Sequence Length:
10
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P10997
Keyword(s):
Islet amyloid polypeptide
Structure Information
PDB ID:
1KUW
Amyloid Category:
Amyloid
Type:
Peptide
Global Stoichiometry:
PDB Classification:
HORMONE/GROWTH FACTOR
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Entry:S-0041
PDB ID: 1LGN
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
H
T
D
L
S
G
K
V
F
V
F
P
R
E
S
V
T
D
H
V
N
L
I
T
P
25
26
L
E
K
P
L
Q
N
F
T
L
C
F
R
A
Y
S
D
L
S
R
A
Y
S
L
F
50
51
S
Y
N
T
Q
G
R
D
N
E
L
L
V
Y
K
E
R
V
G
E
Y
S
L
Y
I
75
76
G
R
H
K
V
T
S
K
V
I
E
K
F
P
A
P
V
H
I
C
V
S
W
E
S
100
101
S
S
G
I
A
E
F
W
I
N
G
T
P
L
V
K
K
G
L
R
Q
G
Y
F
V
125
126
E
A
Q
P
K
I
V
L
G
Q
E
Q
D
S
Y
G
G
K
F
D
R
S
Q
S
F
150
151
V
G
E
I
G
D
L
Y
M
W
D
S
V
L
P
P
E
N
I
L
S
A
Y
Q
G
175
176
T
P
L
P
A
N
I
L
D
W
Q
A
L
N
Y
E
I
R
G
Y
V
I
I
K
P
200
201
L
V
W
V
204
Chain 2
1
H
T
D
L
S
G
K
V
F
V
F
P
R
E
S
V
T
D
H
V
N
L
I
T
P
25
26
L
E
K
P
L
Q
N
F
T
L
C
F
R
A
Y
S
D
L
S
R
A
Y
S
L
F
50
51
S
Y
N
T
Q
G
R
D
N
E
L
L
V
Y
K
E
R
V
G
E
Y
S
L
Y
I
75
76
G
R
H
K
V
T
S
K
V
I
E
K
F
P
A
P
V
H
I
C
V
S
W
E
S
100
101
S
S
G
I
A
E
F
W
I
N
G
T
P
L
V
K
K
G
L
R
Q
G
Y
F
V
125
126
E
A
Q
P
K
I
V
L
G
Q
E
Q
D
S
Y
G
G
K
F
D
R
S
Q
S
F
150
151
V
G
E
I
G
D
L
Y
M
W
D
S
V
L
P
P
E
N
I
L
S
A
Y
Q
G
175
176
T
P
L
P
A
N
I
L
D
W
Q
A
L
N
Y
E
I
R
G
Y
V
I
I
K
P
200
201
L
V
W
V
204
Chain 3
1
H
T
D
L
S
G
K
V
F
V
F
P
R
E
S
V
T
D
H
V
N
L
I
T
P
25
26
L
E
K
P
L
Q
N
F
T
L
C
F
R
A
Y
S
D
L
S
R
A
Y
S
L
F
50
51
S
Y
N
T
Q
G
R
D
N
E
L
L
V
Y
K
E
R
V
G
E
Y
S
L
Y
I
75
76
G
R
H
K
V
T
S
K
V
I
E
K
F
P
A
P
V
H
I
C
V
S
W
E
S
100
101
S
S
G
I
A
E
F
W
I
N
G
T
P
L
V
K
K
G
L
R
Q
G
Y
F
V
125
126
E
A
Q
P
K
I
V
L
G
Q
E
Q
D
S
Y
G
G
K
F
D
R
S
Q
S
F
150
151
V
G
E
I
G
D
L
Y
M
W
D
S
V
L
P
P
E
N
I
L
S
A
Y
Q
G
175
176
T
P
L
P
A
N
I
L
D
W
Q
A
L
N
Y
E
I
R
G
Y
V
I
I
K
P
200
201
L
V
W
V
204
Chain 4
1
H
T
D
L
S
G
K
V
F
V
F
P
R
E
S
V
T
D
H
V
N
L
I
T
P
25
26
L
E
K
P
L
Q
N
F
T
L
C
F
R
A
Y
S
D
L
S
R
A
Y
S
L
F
50
51
S
Y
N
T
Q
G
R
D
N
E
L
L
V
Y
K
E
R
V
G
E
Y
S
L
Y
I
75
76
G
R
H
K
V
T
S
K
V
I
E
K
F
P
A
P
V
H
I
C
V
S
W
E
S
100
101
S
S
G
I
A
E
F
W
I
N
G
T
P
L
V
K
K
G
L
R
Q
G
Y
F
V
125
126
E
A
Q
P
K
I
V
L
G
Q
E
Q
D
S
Y
G
G
K
F
D
R
S
Q
S
F
150
151
V
G
E
I
G
D
L
Y
M
W
D
S
V
L
P
P
E
N
I
L
S
A
Y
Q
G
175
176
T
P
L
P
A
N
I
L
D
W
Q
A
L
N
Y
E
I
R
G
Y
V
I
I
K
P
200
201
L
V
W
V
204
Chain 5
1
H
T
D
L
S
G
K
V
F
V
F
P
R
E
S
V
T
D
H
V
N
L
I
T
P
25
26
L
E
K
P
L
Q
N
F
T
L
C
F
R
A
Y
S
D
L
S
R
A
Y
S
L
F
50
51
S
Y
N
T
Q
G
R
D
N
E
L
L
V
Y
K
E
R
V
G
E
Y
S
L
Y
I
75
76
G
R
H
K
V
T
S
K
V
I
E
K
F
P
A
P
V
H
I
C
V
S
W
E
S
100
101
S
S
G
I
A
E
F
W
I
N
G
T
P
L
V
K
K
G
L
R
Q
G
Y
F
V
125
126
E
A
Q
P
K
I
V
L
G
Q
E
Q
D
S
Y
G
G
K
F
D
R
S
Q
S
F
150
151
V
G
E
I
G
D
L
Y
M
W
D
S
V
L
P
P
E
N
I
L
S
A
Y
Q
G
175
176
T
P
L
P
A
N
I
L
D
W
Q
A
L
N
Y
E
I
R
G
Y
V
I
I
K
P
200
201
L
V
W
V
204
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of a decameric complex of human serum amyloid P component with bound dAMP
Small-molecule ligands that displace SAP from amyloid fibrils and thereby expose the fibrils to proteolytic clearance mechanisms hold potential as drugs for the prevention and treatment of amyloidosis. 2'-deoxyadenosine-5'-monophosphate (dAMP) was screened as a novel SAP ligand. The crystal structure of the SAP-dAMP complex reveals a decamer in which all interactions between SAP pentamers are mediated by the ligand. The two calcium ions of SAP are bridged by the dAMP phosphate group and five hydrogen bonds are formed between the protein and the ligand, including specific interactions made by the adenine base. The SAP-dAMP decamer is stabilized mainly by base-stacking of adjacent ligand molecules and possibly by electrostatic interactions involving the dAMP phosphate groups.
Literature
PMID:
9217261
Author(s):
Hohenester, E., Hutchinson, W.L., Pepys, M.B., Wood, S.P.
Reference:
J Mol Biol. 1997 Jun 20;269(4):570-8
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Structure:
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Contact Network:
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Protein Information
Protein Name:
Serum amyloid P-component
Alternative Name:
9.5S alpha-1-glycoprotein
Gene Name:
APCS, PTX2
Sequence Length:
204
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P02743
Keyword(s):
SERUM AMYLOID P COMPONENT
Structure Information
PDB ID:
1LGN
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Homo 5-mer - A5
PDB Classification:
SERUM PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.8
R free:
0.252
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
CA
A
Ca 2
40.08
CALCIUM ION
[Ca+2]
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
DA
A
C10 H14 N5 O6 P
331.22
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N
KHWCHTKSEGGWEX-RRKCRQDMSA-N
CA
B
Ca 2
40.08
CALCIUM ION
[Ca+2]
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
DA
B
C10 H14 N5 O6 P
331.22
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N
KHWCHTKSEGGWEX-RRKCRQDMSA-N
CA
C
Ca 2
40.08
CALCIUM ION
[Ca+2]
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
DA
C
C10 H14 N5 O6 P
331.22
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N
KHWCHTKSEGGWEX-RRKCRQDMSA-N
CA
D
Ca 2
40.08
CALCIUM ION
[Ca+2]
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
DA
D
C10 H14 N5 O6 P
331.22
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N
KHWCHTKSEGGWEX-RRKCRQDMSA-N
CA
E
Ca 2
40.08
CALCIUM ION
[Ca+2]
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
DA
E
C10 H14 N5 O6 P
331.22
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N
KHWCHTKSEGGWEX-RRKCRQDMSA-N
Entry:S-0042
PDB ID: 1LOZ
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
K
V
F
E
R
C
E
L
A
R
T
L
K
R
L
G
M
D
G
Y
R
G
I
S
L
25
26
A
N
W
M
C
L
A
K
W
E
S
G
Y
N
T
R
A
T
N
Y
N
A
G
D
R
50
51
S
T
D
Y
G
T
F
Q
I
N
S
R
Y
W
C
N
D
G
K
T
P
G
A
V
N
75
76
A
C
H
L
S
C
S
A
L
L
Q
D
N
I
A
D
A
V
A
C
A
K
R
V
V
100
101
R
D
P
Q
G
I
R
A
W
V
A
W
R
N
R
C
Q
N
R
D
V
R
Q
Y
V
125
126
Q
G
C
G
V
130
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
AMYLOIDOGENIC VARIANT (I56T) VARIANT OF HUMAN LYSOZYME
The naturally occurring human lysozyme variants is amyloidogenic, and shown here to be unstable. This aggregates to form amyloid fibrils with transformation of the mainly helical native fold, observed in crystal structures, to the amyloid fibril cross-Beta fold. Biophysical studies suggest that partly folded intermediates are involved in fibrillogenesis
Literature
PMID:
9039909
Author(s):
Booth, D.R., Sunde, M., Bellotti, V., Robinson, C.V., Hutchinson, W.L., Fraser, P.E., Hawkins, P.N., Dobson, C.M., Radford, S.E., Blake, C.C., Pepys, M.B.
Reference:
Nature. 1997 Feb 27;385(6619):787-93
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Entry:
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Structure:
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FASTA
Contact Network:
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Protein Information
Protein Name:
Lysozyme C
Alternative Name:
1, 4-beta-N-acetylmuramidase C
Gene Name:
LYZ, LZM
Sequence Length:
130
Species:
Homo sapiens
Mutation(s):
I56T
E.C. Number:
3.2.1.17
UniProt ID:
P61626
Keyword(s):
LYSOZYME
Structure Information
PDB ID:
1LOZ
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
HYDROLASE
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.8
R free:
Entry:S-0043
PDB ID: 1LYY
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Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
K
V
F
E
R
C
E
L
A
R
T
L
K
R
L
G
M
D
G
Y
R
G
I
S
L
25
26
A
N
W
M
C
L
A
K
W
E
S
G
Y
N
T
R
A
T
N
Y
N
A
G
D
R
50
51
S
T
D
Y
G
I
F
Q
I
N
S
R
Y
W
C
N
H
G
K
T
P
G
A
V
N
75
76
A
C
H
L
S
C
S
A
L
L
Q
D
N
I
A
D
A
V
A
C
A
K
R
V
V
100
101
R
D
P
Q
G
I
R
A
W
V
A
W
R
N
R
C
Q
N
R
D
V
R
Q
Y
V
125
126
Q
G
C
G
V
130
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
AMYLOIDOGENIC VARIANT (ASP67HIS) OF HUMAN LYSOZYME
The naturally occurring human lysozyme variants is amyloidogenic, and shown here to be unstable. This aggregates to form amyloid fibrils with transformation of the mainly helical native fold, observed in crystal structures, to the amyloid fibril cross-Beta fold. Biophysical studies suggest that partly folded intermediates are involved in fibrillogenesis
Literature
PMID:
9039909
Author(s):
Booth, D.R., Sunde, M., Bellotti, V., Robinson, C.V., Hutchinson, W.L., Fraser, P.E., Hawkins, P.N., Dobson, C.M., Radford, S.E., Blake, C.C., Pepys, M.B.
Reference:
Nature. 1997 Feb 27;385(6619):787-93
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Structure:
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Contact Network:
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Protein Information
Protein Name:
Lysozyme C
Alternative Name:
1, 4-beta-N-acetylmuramidase C
Gene Name:
LYZ, LZM
Sequence Length:
130
Species:
Homo sapiens
Mutation(s):
D67H
E.C. Number:
3.2.1.17
UniProt ID:
P61626
Keyword(s):
LYSOZYME
Structure Information
PDB ID:
1LYY
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
HYDROLASE
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.8
R free:
Entry:S-0044
PDB ID: 1N9J
CSV
JSON
Close ×
Structure
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Sequence & Sec. Str.
Chain 1
1
M
I
P
G
G
L
S
E
A
K
P
A
T
P
E
I
Q
E
I
V
D
K
V
K
P
25
26
Q
L
E
E
K
T
N
E
T
Y
G
K
L
E
A
V
Q
Y
K
T
Q
V
V
A
G
50
51
T
N
Y
Y
I
K
V
R
A
G
D
N
K
Y
M
H
L
K
V
F
K
S
L
P
G
75
76
Q
N
E
D
L
V
L
T
G
Y
Q
V
D
K
N
K
D
D
E
L
T
G
F
98
Chain 2
1
M
I
P
G
G
L
S
E
A
K
P
A
T
P
E
I
Q
E
I
V
D
K
V
K
P
25
26
Q
L
E
E
K
T
N
E
T
Y
G
K
L
E
A
V
Q
Y
K
T
Q
V
V
A
G
50
51
T
N
Y
Y
I
K
V
R
A
G
D
N
K
Y
M
H
L
K
V
F
K
S
L
P
G
75
76
Q
N
E
D
L
V
L
T
G
Y
Q
V
D
K
N
K
D
D
E
L
T
G
F
98
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Three-dimensional domain swapping in the folded and molten-globule states of cystatins, an amyloid-forming structural superfamily
Cystatins, an amyloid-forming structural superfamily, form highly stable, domain-swapped dimers at physiological protein concentrations. Destabilization of the folded state shorten the lifetime of the monomeric form. In such circumstances, amyloidogenesis will start from conditions where a domain-swapped dimer is the most prevalent species. Domain swapping occurs by a rearrangement of loop I, generating the new intermonomer interface between strands 2 and 3. Dimerization also occurs when chicken cystatin is in its reduced, molten-globule state, implying that the organization of secondary structure in this state mirrors that in the folded state and that domain swapping is not limited to the folded states of proteins.
Literature
PMID:
11532941
Author(s):
Staniforth, R.A., Giannini, S., Higgins, L.D., Conroy, M.J., Hounslow, A.M., Jerala, R., Craven, C.J., Waltho, J.P.
Reference:
EMBO J. 2001 Sep 3;20(17):4774-81
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Protein Information
Protein Name:
Cystatin-A
Alternative Name:
Cystatin-AS, Stefin-A
Gene Name:
CSTA, STF1, STFA
Sequence Length:
98
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P01040
Keyword(s):
Cystatin A
Structure Information
PDB ID:
1N9J
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
HYDROLASE INHIBITOR
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Entry:S-0045
PDB ID: 1NMJ
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Sequence & Sec. Str.
Chain 1
1
D
A
E
F
G
H
D
S
G
F
E
V
R
H
Q
K
L
V
F
F
A
E
D
V
G
25
26
S
N
K
28
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
The Solution Structure of Rat Ab-(1-28) and its Interaction with Zinc: Insights into the Scarity of Amyloid Deposition in Aged Rat Brain
The three-dimensional solution structure of rat ABeta-(1-28) is more stable than that of human ABeta-(1-28) in DMSO- d(6) and helical region from Glu16 to Val24 exists in the rat ABeta-(1-28). The affinity of Zn(2+) for rat ABeta-(1-28) is lower than that for human ABeta-(1-28) and the NMR data suggest that Arg13, His6, and His14 residues provide the primary binding sites for Zn(2+). The proper binding of Zn(2+) to rat ABeta-(1-28) can induce the peptide to change to a more stable conformation.
Literature
PMID:
15160315
Author(s):
Huang, J., Yao, Y., Lin, J., Ye, Y.H., Sun, W.Y., Tang, W.X.
Reference:
J Biol Inorg Chem. 2004 Jul;9(5):627-35. Epub 2004 May 25
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Entry:
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Protein Information
Protein Name:
Amyloid-beta A4 protein
Alternative Name:
ABPP, Alzheimer disease amyloid A4 protein homolog, Amyloid precursor protein, Amyloid-beta precursor protein, Amyloidogenic glycoprotein
Gene Name:
App
Sequence Length:
28
Species:
Rattus norvegicus
Mutation(s):
No
E.C. Number:
UniProt ID:
P08592
Keyword(s):
amyloid beta-peptide from Alzheimer's disease amyloid A4 protein homolog
Structure Information
PDB ID:
1NMJ
Amyloid Category:
Non-amyloid
Type:
Peptide
Global Stoichiometry:
Monomer - A
PDB Classification:
MEMBRANE PROTEIN
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Entry:S-0046
PDB ID: 1OEZ
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
A
T
K
A
V
C
V
L
K
G
D
G
P
V
Q
G
I
I
N
F
E
Q
K
E
S
25
26
N
G
P
V
K
V
W
G
S
I
K
G
L
T
E
G
L
H
G
F
R
V
H
E
F
50
51
G
D
N
T
A
G
C
T
S
A
G
P
H
F
N
P
L
S
R
K
H
G
G
P
K
75
76
D
E
E
R
H
V
G
D
L
G
N
V
T
A
D
K
D
G
V
A
D
V
S
I
E
100
101
D
S
V
I
S
L
S
G
D
H
C
I
I
G
R
T
L
V
V
H
E
K
A
D
D
125
126
L
G
K
G
G
N
E
E
S
T
K
T
G
N
A
G
S
R
L
A
C
G
V
I
G
150
151
I
A
Q
153
Chain 2
1
A
T
K
A
V
C
V
L
K
G
D
G
P
V
Q
G
I
I
N
F
E
Q
K
E
S
25
26
N
G
P
V
K
V
W
G
S
I
K
G
L
T
E
G
L
H
G
F
R
V
H
E
F
50
51
G
D
N
T
A
G
C
T
S
A
G
P
H
F
N
P
L
S
R
K
H
G
G
P
K
75
76
D
E
E
R
H
V
G
D
L
G
N
V
T
A
D
K
D
G
V
A
D
V
S
I
E
100
101
D
S
V
I
S
L
S
G
D
H
C
I
I
G
R
T
L
V
V
H
E
K
A
D
D
125
126
L
G
K
G
G
N
E
E
S
T
K
T
G
N
A
G
S
R
L
A
C
G
V
I
G
150
151
I
A
Q
153
Chain 3
1
A
T
K
A
V
C
V
L
K
G
D
G
P
V
Q
G
I
I
N
F
E
Q
K
E
S
25
26
N
G
P
V
K
V
W
G
S
I
K
G
L
T
E
G
L
H
G
F
R
V
H
E
F
50
51
G
D
N
T
A
G
C
T
S
A
G
P
H
F
N
P
L
S
R
K
H
G
G
P
K
75
76
D
E
E
R
H
V
G
D
L
G
N
V
T
A
D
K
D
G
V
A
D
V
S
I
E
100
101
D
S
V
I
S
L
S
G
D
H
C
I
I
G
R
T
L
V
V
H
E
K
A
D
D
125
126
L
G
K
G
G
N
E
E
S
T
K
T
G
N
A
G
S
R
L
A
C
G
V
I
G
150
151
I
A
Q
153
Chain 4
1
A
T
K
A
V
C
V
L
K
G
D
G
P
V
Q
G
I
I
N
F
E
Q
K
E
S
25
26
N
G
P
V
K
V
W
G
S
I
K
G
L
T
E
G
L
H
G
F
R
V
H
E
F
50
51
G
D
N
T
A
G
C
T
S
A
G
P
H
F
N
P
L
S
R
K
H
G
G
P
K
75
76
D
E
E
R
H
V
G
D
L
G
N
V
T
A
D
K
D
G
V
A
D
V
S
I
E
100
101
D
S
V
I
S
L
S
G
D
H
C
I
I
G
R
T
L
V
V
H
E
K
A
D
D
125
126
L
G
K
G
G
N
E
E
S
T
K
T
G
N
A
G
S
R
L
A
C
G
V
I
G
150
151
I
A
Q
153
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Zn His46Arg mutant of Human Cu, Zn Superoxide Dismutase; water-filled nanotubes
The observation of the hollow, pore-like structure formed by Zn–H46R is particularly intriguing because 'amyloid pores' are observed in mutants of Alpha-synuclein and Beta-amyloid. all Zn–H46R subunits have zinc bound in their Zn-binding sites but no metal in their Cu-binding sites
Literature
PMID:
12754496
Author(s):
Elam, J.S., Taylor, A.B., Strange, R.W., Antonyuk, S., Doucette, P., Rodriguez, J., Hasnain, S.S., Hayward, L.J., Valentine, J.S., Yeates, T.O., Hart, P.J.
Reference:
Nat Struct Biol. 2003 Jun;10(6):461-7
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Protein Information
Protein Name:
Superoxide dismutase [Cu-Zn]
Alternative Name:
Superoxide dismutase 1
Gene Name:
SOD1
Sequence Length:
153
Species:
Homo sapiens
Mutation(s):
Zn-H46R
E.C. Number:
1.15.1.1
UniProt ID:
P00441
Keyword(s):
SUPEROXIDE DISMUTASE [CU-ZN]
Structure Information
PDB ID:
1OEZ
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
OXIDOREDUCTASE
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.15
R free:
0.23399999
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
SO4
W
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
W
Zn 2
65.41
ZINC ION
[Zn+2]
PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4
X
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
X
Zn 2
65.41
ZINC ION
[Zn+2]
PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4
Y
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Y
Zn 2
65.41
ZINC ION
[Zn+2]
PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4
Z
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Z
Zn 2
65.41
ZINC ION
[Zn+2]
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Entry:S-0047
PDB ID: 1OP9
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
Q
V
Q
L
Q
E
S
G
G
G
S
V
Q
A
G
G
S
L
R
L
S
C
S
A
S
25
26
G
Y
T
Y
I
S
G
W
F
R
Q
A
P
G
K
E
R
E
G
V
A
A
I
R
S
50
51
S
D
G
T
T
Y
Y
A
D
S
V
K
G
R
F
T
I
S
Q
D
N
A
K
N
T
75
76
V
Y
L
Q
M
N
S
L
K
P
E
D
T
A
M
Y
Y
C
A
A
T
E
V
A
G
100
101
W
P
L
D
I
G
I
Y
D
Y
W
G
Q
G
T
E
V
T
V
S
S
121
Chain 2
1
K
V
F
E
R
C
E
L
A
R
T
L
K
R
L
G
M
D
G
Y
R
G
I
S
L
25
26
A
N
W
M
C
L
A
K
W
E
S
G
Y
N
T
R
A
T
N
Y
N
A
G
D
R
50
51
S
T
D
Y
G
I
F
Q
I
N
S
R
Y
W
C
N
D
G
K
T
P
G
A
V
N
75
76
A
C
H
L
S
C
S
A
L
L
Q
D
N
I
A
D
A
V
A
C
A
K
R
V
V
100
101
R
D
P
Q
G
I
R
A
W
V
A
W
R
N
R
C
Q
N
R
D
V
R
Q
Y
V
125
126
Q
G
C
G
V
130
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Complex of human lysozyme with camelid VHH HL6 antibody fragment
A single-domain fragment of a camelid antibody raised against wild-type human lysozyme inhibits the in vitro aggregation of its amyloidogenic variant, D67H. The structural study reveals that the binding of the antibody fragment achieves its effect by restoring the structural cooperativity characteristic of the wild-type protein. This appears to occur at least in part through the transmission of long-range conformational effects to the interface between the two structural domains of the protein. Reducing the ability of an amyloidogenic protein to form partly unfolded species can be an effective method of preventing its aggregation.
Literature
PMID:
12917687
Author(s):
Dumoulin, M., Last, A.M., Desmyter, A., Decanniere, K., Canet, D., Larsson, G., Spencer, A., Archer, D.B., Sasse, J., Muyldermans, S., Wyns, L., Redfield, C., Matagne, A., Robinson, C.V., Dobson, C.M.
Reference:
Nature. 2003 Aug 14;424(6950):783-8
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Protein Information
Protein Name:
lysozyme
Alternative Name:
1, 4-beta-N-acetylmuramidase C
Gene Name:
LYZ, LZM
Sequence Length:
121 , 130
Species:
Mutation(s):
No
E.C. Number:
3.2.1.17
UniProt ID:
Keyword(s):
Structure Information
PDB ID:
1OP9
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Hetero 2-mer - AB
PDB Classification:
HYDROLASE
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.86
R free:
0.23800000
Entry:S-0048
PDB ID: 1OUA
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Sequence & Sec. Str.
Chain 1
1
K
V
F
E
R
C
E
L
A
R
T
L
K
R
L
G
M
D
G
Y
R
G
I
S
L
25
26
A
N
W
M
C
L
A
K
W
E
S
G
Y
N
T
R
A
T
N
Y
N
A
G
D
R
50
51
S
T
D
Y
G
T
F
Q
I
N
S
R
Y
W
C
N
D
G
K
T
P
G
A
V
N
75
76
A
C
H
L
S
C
S
A
L
L
Q
D
N
I
A
D
A
V
A
C
A
K
R
V
V
100
101
R
D
P
Q
G
I
R
A
W
V
A
W
R
N
R
C
Q
N
R
D
V
R
Q
Y
V
125
126
Q
G
C
G
V
130
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
CONTRIBUTION OF HYDROPHOBIC RESIDUES TO THE STABILITY OF HUMAN LYSOZYME: X-RAY STRUCTURE OF THE I56T MUTANT
The crystal structure of the mutant protein was the same as the wild-type structure, except that the hydroxyl group of the introduced Thr56 formed a hydrogen bond with a water molecule in the interior of the protein. The other physicochemical properties of the mutant protein in the native state were not different from those of the wild-type protein. However, the equilibrium and kinetic stabilities of the mutant protein were remarkably decreased due to the introduction of a polar residue (Thr) in the interior of the molecule. It can be concluded that the amyloid formation of the mutant human lysozyme is due to a tendency to favor (partly or/and completely) denatured structures.
Literature
PMID:
9010773
Author(s):
Funahashi, J., Takano, K., Ogasahara, K., Yamagata, Y., Yutani, K.
Reference:
J Biochem. 1996 Dec;120(6):1216-23
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Protein Information
Protein Name:
Lysozyme C
Alternative Name:
1, 4-beta-N-acetylmuramidase C
Gene Name:
LYZ, LZM
Sequence Length:
130
Species:
Homo sapiens
Mutation(s):
I56T
E.C. Number:
3.2.1.17
UniProt ID:
P61626
Keyword(s):
LYSOZYME
Structure Information
PDB ID:
1OUA
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
HYDROLASE (O-GLYCOSYL)
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.8
R free:
Entry:S-0049
PDB ID: 1OZT
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Sequence & Sec. Str.
Chain 1
1
A
T
K
A
V
C
V
L
K
G
D
G
P
V
Q
G
I
I
N
F
E
Q
K
E
S
25
26
N
G
P
V
K
V
W
G
S
I
K
G
L
T
E
G
L
H
G
F
R
V
H
E
F
50
51
G
D
N
T
A
G
C
T
S
A
G
P
H
F
N
P
L
S
R
K
H
G
G
P
K
75
76
D
E
E
R
H
V
G
D
L
G
N
V
T
A
D
K
D
G
V
A
D
V
S
I
E
100
101
D
S
V
I
S
L
S
G
D
H
C
I
I
G
R
T
L
V
V
H
E
K
A
D
D
125
126
L
G
K
G
G
N
E
E
S
T
K
T
G
N
A
G
S
R
L
A
C
G
V
I
G
150
151
I
A
Q
153
Chain 2
1
A
T
K
A
V
C
V
L
K
G
D
G
P
V
Q
G
I
I
N
F
E
Q
K
E
S
25
26
N
G
P
V
K
V
W
G
S
I
K
G
L
T
E
G
L
H
G
F
R
V
H
E
F
50
51
G
D
N
T
A
G
C
T
S
A
G
P
H
F
N
P
L
S
R
K
H
G
G
P
K
75
76
D
E
E
R
H
V
G
D
L
G
N
V
T
A
D
K
D
G
V
A
D
V
S
I
E
100
101
D
S
V
I
S
L
S
G
D
H
C
I
I
G
R
T
L
V
V
H
E
K
A
D
D
125
126
L
G
K
G
G
N
E
E
S
T
K
T
G
N
A
G
S
R
L
A
C
G
V
I
G
150
151
I
A
Q
153
Chain 3
1
A
T
K
A
V
C
V
L
K
G
D
G
P
V
Q
G
I
I
N
F
E
Q
K
E
S
25
26
N
G
P
V
K
V
W
G
S
I
K
G
L
T
E
G
L
H
G
F
R
V
H
E
F
50
51
G
D
N
T
A
G
C
T
S
A
G
P
H
F
N
P
L
S
R
K
H
G
G
P
K
75
76
D
E
E
R
H
V
G
D
L
G
N
V
T
A
D
K
D
G
V
A
D
V
S
I
E
100
101
D
S
V
I
S
L
S
G
D
H
C
I
I
G
R
T
L
V
V
H
E
K
A
D
D
125
126
L
G
K
G
G
N
E
E
S
T
K
T
G
N
A
G
S
R
L
A
C
G
V
I
G
150
151
I
A
Q
153
Chain 4
1
A
T
K
A
V
C
V
L
K
G
D
G
P
V
Q
G
I
I
N
F
E
Q
K
E
S
25
26
N
G
P
V
K
V
W
G
S
I
K
G
L
T
E
G
L
H
G
F
R
V
H
E
F
50
51
G
D
N
T
A
G
C
T
S
A
G
P
H
F
N
P
L
S
R
K
H
G
G
P
K
75
76
D
E
E
R
H
V
G
D
L
G
N
V
T
A
D
K
D
G
V
A
D
V
S
I
E
100
101
D
S
V
I
S
L
S
G
D
H
C
I
I
G
R
T
L
V
V
H
E
K
A
D
D
125
126
L
G
K
G
G
N
E
E
S
T
K
T
G
N
A
G
S
R
L
A
C
G
V
I
G
150
151
I
A
Q
153
Chain 5
1
A
T
K
A
V
C
V
L
K
G
D
G
P
V
Q
G
I
I
N
F
E
Q
K
E
S
25
26
N
G
P
V
K
V
W
G
S
I
K
G
L
T
E
G
L
H
G
F
R
V
H
E
F
50
51
G
D
N
T
A
G
C
T
S
A
G
P
H
F
N
P
L
S
R
K
H
G
G
P
K
75
76
D
E
E
R
H
V
G
D
L
G
N
V
T
A
D
K
D
G
V
A
D
V
S
I
E
100
101
D
S
V
I
S
L
S
G
D
H
C
I
I
G
R
T
L
V
V
H
E
K
A
D
D
125
126
L
G
K
G
G
N
E
E
S
T
K
T
G
N
A
G
S
R
L
A
C
G
V
I
G
150
151
I
A
Q
153
Chain 6
1
A
T
K
A
V
C
V
L
K
G
D
G
P
V
Q
G
I
I
N
F
E
Q
K
E
S
25
26
N
G
P
V
K
V
W
G
S
I
K
G
L
T
E
G
L
H
G
F
R
V
H
E
F
50
51
G
D
N
T
A
G
C
T
S
A
G
P
H
F
N
P
L
S
R
K
H
G
G
P
K
75
76
D
E
E
R
H
V
G
D
L
G
N
V
T
A
D
K
D
G
V
A
D
V
S
I
E
100
101
D
S
V
I
S
L
S
G
D
H
C
I
I
G
R
T
L
V
V
H
E
K
A
D
D
125
126
L
G
K
G
G
N
E
E
S
T
K
T
G
N
A
G
S
R
L
A
C
G
V
I
G
150
151
I
A
Q
153
Chain 7
1
A
T
K
A
V
C
V
L
K
G
D
G
P
V
Q
G
I
I
N
F
E
Q
K
E
S
25
26
N
G
P
V
K
V
W
G
S
I
K
G
L
T
E
G
L
H
G
F
R
V
H
E
F
50
51
G
D
N
T
A
G
C
T
S
A
G
P
H
F
N
P
L
S
R
K
H
G
G
P
K
75
76
D
E
E
R
H
V
G
D
L
G
N
V
T
A
D
K
D
G
V
A
D
V
S
I
E
100
101
D
S
V
I
S
L
S
G
D
H
C
I
I
G
R
T
L
V
V
H
E
K
A
D
D
125
126
L
G
K
G
G
N
E
E
S
T
K
T
G
N
A
G
S
R
L
A
C
G
V
I
G
150
151
I
A
Q
153
Chain 8
1
A
T
K
A
V
C
V
L
K
G
D
G
P
V
Q
G
I
I
N
F
E
Q
K
E
S
25
26
N
G
P
V
K
V
W
G
S
I
K
G
L
T
E
G
L
H
G
F
R
V
H
E
F
50
51
G
D
N
T
A
G
C
T
S
A
G
P
H
F
N
P
L
S
R
K
H
G
G
P
K
75
76
D
E
E
R
H
V
G
D
L
G
N
V
T
A
D
K
D
G
V
A
D
V
S
I
E
100
101
D
S
V
I
S
L
S
G
D
H
C
I
I
G
R
T
L
V
V
H
E
K
A
D
D
125
126
L
G
K
G
G
N
E
E
S
T
K
T
G
N
A
G
S
R
L
A
C
G
V
I
G
150
151
I
A
Q
153
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal Structure of apo-H46R Familial ALS Mutant human Cu,Zn Superoxide Dismutase (CuZnSOD); linear amyloid-like filaments
H46R SOD1 structure is preserve relative to the wild-type protein, it exhibit significant disorder and conformational change in its zinc and electrostatic loop elements. Amyloid-like filaments of pathogenic SOD1 dimers are linear. Residues 125–131 of the electrostatic loop adopt an extended, non-native conformation and participate in extensive hydrogen bonding and apolar interactions with the deprotected surface depression on the Beta-barrel of a neighboring SOD1 dimer. apo-H46R subunits are completely devoid of both copper and zinc ions in their binding sites.
Literature
PMID:
12754496
Author(s):
Elam, J.S., Taylor, A.B., Strange, R., Antonyuk, S., Doucette, P.A., Rodriguez, J.A., Hasnain, S.S., Hayward, L.J., Valentine, J.S., Yeates, T.O., Hart, P.J.
Reference:
Nat Struct Biol. 2003 Jun;10(6):461-7
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Entry:
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Structure:
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CIF
FASTA
Contact Network:
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Protein Information
Protein Name:
Superoxide dismutase [Cu-Zn]
Alternative Name:
Superoxide dismutase 1
Gene Name:
SOD1
Sequence Length:
153
Species:
Homo sapiens
Mutation(s):
apo-H46R
E.C. Number:
1.15.1.1
UniProt ID:
P00441
Keyword(s):
Superoxide dismutase [Cu-Zn]
Structure Information
PDB ID:
1OZT
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
OXIDOREDUCTASE
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.5
R free:
0.27
Entry:S-0050
PDB ID: 1OZU
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JSON
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
A
T
K
A
V
C
V
L
K
G
D
G
P
V
Q
G
I
I
N
F
E
Q
K
E
S
25
26
N
G
P
V
K
V
W
G
S
I
K
G
L
T
E
G
L
H
G
F
H
V
H
E
F
50
51
G
D
N
T
A
G
C
T
S
A
G
P
H
F
N
P
L
S
R
K
H
G
G
P
K
75
76
D
E
E
R
H
V
G
D
L
G
N
V
T
A
D
K
D
G
V
A
D
V
S
I
E
100
101
D
S
V
I
S
L
S
G
D
H
C
I
I
G
R
T
L
V
V
H
E
K
A
D
D
125
126
L
G
K
G
G
N
E
E
N
T
K
T
G
N
A
G
S
R
L
A
C
G
V
I
G
150
151
I
A
Q
153
Chain 2
1
A
T
K
A
V
C
V
L
K
G
D
G
P
V
Q
G
I
I
N
F
E
Q
K
E
S
25
26
N
G
P
V
K
V
W
G
S
I
K
G
L
T
E
G
L
H
G
F
H
V
H
E
F
50
51
G
D
N
T
A
G
C
T
S
A
G
P
H
F
N
P
L
S
R
K
H
G
G
P
K
75
76
D
E
E
R
H
V
G
D
L
G
N
V
T
A
D
K
D
G
V
A
D
V
S
I
E
100
101
D
S
V
I
S
L
S
G
D
H
C
I
I
G
R
T
L
V
V
H
E
K
A
D
D
125
126
L
G
K
G
G
N
E
E
N
T
K
T
G
N
A
G
S
R
L
A
C
G
V
I
G
150
151
I
A
Q
153
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal Structure of Familial ALS Mutant S134N of human Cu,Zn Superoxide Dismutase (CuZnSOD)
S134N SOD1 structure is preserve relative to the wild-type protein, it exhibit significant disorder and conformational change in its zinc and electrostatic loop elements. Amyloid-like filaments of pathogenic SOD1 dimers are linear. Residues 125–131 of the electrostatic loop adopt an extended, non-native conformation and participate in extensive hydrogen bonding and apolar interactions with the deprotected surface depression on the Beta-barrel of a neighboring SOD1 dimer. There is a mixture of copper and zinc ions in the Cu-binding site and zinc alone is bound in the Zn-binding site in the subunits of S134N SOD1.
Literature
PMID:
12754496
Author(s):
Elam, J.S., Taylor, A.B., Strange, R., Antonyuk, S., Doucette, P.A., Rodriguez, J.A., Hasnain, S.S., Hayward, L.J., Valentine, J.S., Yeates, T.O., Hart, P.J.
Reference:
Nat Struct Biol. 2003 Jun;10(6):461-7
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Superoxide dismutase [Cu-Zn]
Alternative Name:
Superoxide dismutase 1
Gene Name:
SOD1
Sequence Length:
153
Species:
Homo sapiens
Mutation(s):
S134N
E.C. Number:
1.15.1.1
UniProt ID:
P00441
Keyword(s):
Superoxide dismutase [Cu-Zn]
Structure Information
PDB ID:
1OZU
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
OXIDOREDUCTASE
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.3
R free:
0.193
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
CSX
A
C3 H7 N O3 S
137.16
S-OXY CYSTEINE
C([C@@H](C(=O)O)N)[S@H]=O
BHLMCOCHAVMHLD-REOHCLBHSA-N
SO4
A
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
A
Zn 2
65.41
ZINC ION
[Zn+2]
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CSX
B
C3 H7 N O3 S
137.16
S-OXY CYSTEINE
C([C@@H](C(=O)O)N)[S@H]=O
BHLMCOCHAVMHLD-REOHCLBHSA-N
SO4
B
O4 S -2
96.06
SULFATE ION
[O-]S(=O)(=O)[O-]
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
B
Zn 2
65.41
ZINC ION
[Zn+2]
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Entry:S-0051
PDB ID: 1PY4
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
M
I
Q
R
T
P
K
I
Q
V
Y
S
R
H
P
A
E
N
G
K
S
N
F
L
N
25
26
C
Y
V
S
G
F
Y
P
S
D
I
E
V
D
L
L
K
N
G
E
R
I
E
K
V
50
51
E
H
S
D
L
S
F
S
K
D
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
D
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Chain 2
1
M
I
Q
R
T
P
K
I
Q
V
Y
S
R
H
P
A
E
N
G
K
S
N
F
L
N
25
26
C
Y
V
S
G
F
Y
P
S
D
I
E
V
D
L
L
K
N
G
E
R
I
E
K
V
50
51
E
H
S
D
L
S
F
S
K
D
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
D
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Chain 3
1
M
I
Q
R
T
P
K
I
Q
V
Y
S
R
H
P
A
E
N
G
K
S
N
F
L
N
25
26
C
Y
V
S
G
F
Y
P
S
D
I
E
V
D
L
L
K
N
G
E
R
I
E
K
V
50
51
E
H
S
D
L
S
F
S
K
D
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
D
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Chain 4
1
M
I
Q
R
T
P
K
I
Q
V
Y
S
R
H
P
A
E
N
G
K
S
N
F
L
N
25
26
C
Y
V
S
G
F
Y
P
S
D
I
E
V
D
L
L
K
N
G
E
R
I
E
K
V
50
51
E
H
S
D
L
S
F
S
K
D
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
75
76
K
D
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
100
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Beta2 microglobulin mutant H31Y displays hints for amyloid formations
the His31Tyr human Beta2m mutant, a non-natural form of Beta2m that is more stable than the wild-type protein, displaying a ten-fold acceleration of the slow phase of folding, was characterized. Juxtaposition of the four mutant Beta2m molecules contained in the crystal asymmetric unit, and specific hydrogen bonds, stabilize a compact protein assembly. Conformational heterogeneity of the four independent molecules, some of their mutual interactions and partial unpairing of the N-terminal Beta-strand in one protomer are in keeping with the amyloidogenic properties displayed by the mutant Beta2m.
Literature
PMID:
14698299
Author(s):
Rosano, C., Zuccotti, S., Mangione, P., Giorgetti, S., Bellotti, V., Pettirossi, F., Corazza, A., Viglino, P., Esposito, G., Bolognesi, M.
Reference:
J Mol Biol. 2004 Jan 23;335(4):1051-64
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Beta-2-microglobulin
Alternative Name:
Gene Name:
B2M, CDABP0092, HDCMA22P
Sequence Length:
100
Species:
Homo sapiens
Mutation(s):
H31Y
E.C. Number:
UniProt ID:
P61769
Keyword(s):
Beta-2-microglobulin precursor
Structure Information
PDB ID:
1PY4
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
SIGNALING PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.9
R free:
0.313
Entry:S-0052
PDB ID: 1Q38
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Sequence & Sec. Str.
Chain 1
1
M
R
G
S
N
A
P
Q
P
S
H
I
S
K
Y
I
L
R
W
R
P
K
N
S
V
25
26
G
R
W
K
E
A
T
I
P
G
H
L
N
S
Y
T
I
K
G
L
K
P
G
V
V
50
51
Y
E
G
Q
L
I
S
I
Q
Q
Y
G
H
Q
E
V
T
R
F
D
F
T
T
T
S
75
76
T
S
T
P
G
S
R
S
H
H
H
H
H
H
89
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Anastellin, an FN3 fragment with fibronectin polymerization activity, resembles amyloid fibril precursors
Anastellin is a carboxy-terminal fragment of the first FN3 domain from human fibronectin. It is capable of polymerizing fibronectin in vitro, and it displays anti-tumor, anti-metastatic and anti-angiogenic properties in vivo. However, its hydrophobic core becomes solvent-accessible and some of its Beta-strands lose their protection against hydrogen bonding to Beta-strands from other molecules. These features seem to be relevant for the fibronectin polymerization activity of anastellin and resemble the characteristics of amyloid fibril precursors.
Literature
PMID:
12946358
Author(s):
Briknarova, K., Akerman, M.E., Hoyt, D.W., Ruoslahti, E., Ely, K.R.
Reference:
J Mol Biol. 2003 Sep 5;332(1):205-15
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Protein Information
Protein Name:
Fibronectin
Alternative Name:
Cold-insoluble globulin
Gene Name:
FN1, FN
Sequence Length:
89
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P02751
Keyword(s):
Fibronectin
Structure Information
PDB ID:
1Q38
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
CELL ADHESION
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Entry:S-0053
PDB ID: 1QCM
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Sequence & Sec. Str.
Chain 1
1
G
S
N
K
G
A
I
I
G
L
M
11
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Three-dimensional structures of the amyloid beta peptide (25-35) in membrane-mimicking environment
The three-dimensional structure of amyloid Beta peptide (25-35), which has neurotoxic activity, in lithium dodecyl sulfate micelles was determined by two-dimensional 1H NMR spectroscopy with simulated annealing calculations. The molecular structure of amyloid Beta peptide in membrane-mimicking environment is composed of a short Alpha helix in the C terminal position. The three residues from the N-terminus are disordered, but the remaining eight C-terminal residues are well-ordered. The four amino acid residues from the N-terminus are hydrophilic and the other seven amino acid residues in C-terminus are hydrophobic. So, our results show that the C-terminal region of amyloid Beta peptide (25-35) is buried in the membrane and assumes Alpha-helical structure, whereas the N-terminal region is exposed to the solvent with a flexible structure.
Literature
PMID:
8973180
Author(s):
Kohno, T., Kobayashi, K., Maeda, T., Sato, K., Takashima, A.
Reference:
Biochemistry. 1996 Dec 17;35(50):16094-104
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Protein Information
Protein Name:
Amyloid-beta A4 protein
Alternative Name:
Gene Name:
Sequence Length:
11
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P05067
Keyword(s):
AMYLOID BETA PEPTIDE
Structure Information
PDB ID:
1QCM
Amyloid Category:
Amyloid
Type:
Peptide
Global Stoichiometry:
PDB Classification:
AMYLOID
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Entry:S-0054
PDB ID: 1QJH
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
M
R
R
Y
E
V
N
I
V
L
N
P
N
L
D
Q
S
Q
L
A
L
E
K
E
I
25
26
I
Q
R
A
L
E
N
Y
G
A
R
V
E
K
V
A
I
L
G
L
M
V
L
A
Y
50
51
P
I
A
K
D
P
Q
G
Y
F
L
W
Y
Q
V
E
M
P
E
D
R
V
N
D
L
75
76
A
R
E
L
R
I
R
D
N
V
R
R
V
M
V
V
K
S
Q
E
P
F
L
A
N
100
101
A
101
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Engineered version of the ribosomal protein S6; EA41/EI42/RM46/RV47 (S6-Alz)
S6-Alz displays complex reversible aggregation in the refolding process and is disposed to form soluble aggregates in its folded state. The crystal structure of S6-Alz shows that the mutated protein assembles into tetramers joined by intermolecular Beta-sheets involving the Beta-AP sequence. Peptides encompassing the engineered sequence readily form fibrils, suggesting a link between transient aggregation, tetramerization, and fibrillation. The onset of aggregation is linked to the deletion of charged residues, which leaves contiguous hydrophobic stretches in the protein's primary sequence.
Literature
PMID:
10944185
Author(s):
Otzen, D.E., Kristensen, O., Oliveberg, M.
Reference:
Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):9907-12
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Protein Information
Protein Name:
30S ribosomal protein S6
Alternative Name:
TS9
Gene Name:
rpsF, rps6
Sequence Length:
101
Species:
Thermus thermophilus
Mutation(s):
E41A/E42I/R46M/R47V
E.C. Number:
UniProt ID:
P23370
Keyword(s):
30S ribosomal protein S6
Structure Information
PDB ID:
1QJH
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
RIBOSOMAL PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.2
R free:
0.275
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
MG
A
Mg 2
24.31
MAGNESIUM ION
[Mg+2]
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Entry:S-0055
PDB ID: 1QP1
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
D
I
Q
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
Q
A
25
26
S
Q
D
I
S
D
Y
L
I
W
Y
Q
Q
K
L
G
K
A
P
N
L
L
I
Y
D
50
51
A
S
T
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
E
Y
T
F
T
I
75
76
S
S
L
Q
P
E
D
I
A
T
Y
Y
C
Q
Q
Y
D
D
L
P
Y
T
F
G
Q
100
101
G
T
K
V
E
I
K
107
Chain 2
1
D
I
Q
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
Q
A
25
26
S
Q
D
I
S
D
Y
L
I
W
Y
Q
Q
K
L
G
K
A
P
N
L
L
I
Y
D
50
51
A
S
T
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
E
Y
T
F
T
I
75
76
S
S
L
Q
P
E
D
I
A
T
Y
Y
C
Q
Q
Y
D
D
L
P
Y
T
F
G
Q
100
101
G
T
K
V
E
I
K
107
Chain 3
1
D
I
Q
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
Q
A
25
26
S
Q
D
I
S
D
Y
L
I
W
Y
Q
Q
K
L
G
K
A
P
N
L
L
I
Y
D
50
51
A
S
T
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
E
Y
T
F
T
I
75
76
S
S
L
Q
P
E
D
I
A
T
Y
Y
C
Q
Q
Y
D
D
L
P
Y
T
F
G
Q
100
101
G
T
K
V
E
I
K
107
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
amyloid-forming Bence-Jones protein kappa I Bre
The molecular structure of the amyloid-forming Bence-Jones protein kappa I Bre has been determined by X-ray crystallography at 2.0 A resolution. The structure can best be described as hollow cylinders of protein with a central core of water that extend through the crystal in the z direction. The resulting structure has many features which have been found or suggested from studies on the protein fibrils found in amyloid deposits. From the results of the X-ray crystal structure a hypothesis is presented for the structure and formation of the amyloid fibril.
Literature
PMID:
9990143
Author(s):
Steinrauf, L.K., Chiang, M.Y., Shiuan, D.
Reference:
J Biochem. 1999 Feb;125(2):422-9
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Protein Information
Protein Name:
Immunoglobulin kappa variable 1-33
Alternative Name:
Ig kappa chain V-I region AU, Ig kappa chain V-I region Ka
Gene Name:
IGKV1-33
Sequence Length:
107
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P01594
Keyword(s):
BENCE-JONES KAPPA I ANTIBODY BRE (LIGHT CHAIN)
Structure Information
PDB ID:
1QP1
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 3-mer - A3
PDB Classification:
IMMUNE SYSTEM
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.06
R free:
0.212
Entry:S-0056
PDB ID: 1QWP
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Sequence & Sec. Str.
Chain 1
1
G
S
N
K
G
A
I
I
G
L
M
11
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
GSNKGAIIGLM, highly toxic synthetic derivative of amyloid beta-peptides
ABeta-(25-35), sequence GSNKGAIIGLM, is a highly toxic synthetic derivative of amyloid Beta-peptides (ABeta-peptides), which forms fibrillary aggregates. ABeta-(25-35) is investigated in a membrane-mimicking environment (HFIP/water 80/20 mixtures). Furthermore, a comparison with the solution structure of full-length amyloid peptides suggests a role for the 25-27 kink region, which appears to be a general feature of all peptides under the solution conditions explored.
Literature
PMID:
15293994
Author(s):
D'Ursi, A.M., Armenante, M.R., Guerrini, R., Salvadori, S., Sorrentino, G., Picone, D.
Reference:
J Med Chem. 2004 Aug 12;47(17):4231-8
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Protein Information
Protein Name:
Amyloid-beta A4 protein
Alternative Name:
Gene Name:
Sequence Length:
11
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P05067
Keyword(s):
11-mer peptide from Amyloid beta A4 protein
Structure Information
PDB ID:
1QWP
Amyloid Category:
Amyloid
Type:
Peptide
Global Stoichiometry:
PDB Classification:
PROTEIN BINDING
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Entry:S-0057
PDB ID: 1QXC
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Sequence & Sec. Str.
Chain 1
1
G
S
N
K
G
A
I
I
G
L
M
11
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
NMR structure of the fragment 25-35 of beta amyloid peptide in 20/80 v:v hexafluoroisopropanol/water mixture
ABeta-(25-35), sequence GSNKGAIIGLM, is a highly toxic synthetic derivative of amyloid Beta-peptides (ABeta-peptides), which forms fibrillary aggregates. ABeta-(25-35) is investigated in a membrane-mimicking environment (HFIP/water 20/80 mixture). Furthermore, a comparison with the solution structure of full-length amyloid peptides suggests a role for the 25-27 kink region, which appears to be a general feature of all peptides under the solution conditions explored.
Literature
PMID:
15293994
Author(s):
D'Ursi, A.M., Armenante, M.R., Guerrini, R., Salvadori, S., Sorrentino, G., Picone, D.
Reference:
J Med Chem. 2004 Aug 12;47(17):4231-8
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Protein Information
Protein Name:
Amyloid-beta A4 protein
Alternative Name:
Gene Name:
Sequence Length:
11
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P05067
Keyword(s):
11-mer peptide from Amyloid beta A4 protein
Structure Information
PDB ID:
1QXC
Amyloid Category:
Amyloid
Type:
Peptide
Global Stoichiometry:
PDB Classification:
PROTEIN BINDING
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Entry:S-0058
PDB ID: 1QYT
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Sequence & Sec. Str.
Chain 1
1
G
S
N
K
G
A
I
I
G
L
M
11
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Solution structure of fragment (25-35) of beta amyloid peptide in SDS micellar solution
ABeta-(25-35), sequence GSNKGAIIGLM, is a highly toxic synthetic derivative of amyloid Beta-peptides (ABeta-peptides), which forms fibrillary aggregates. ABeta-(25-35) is investigated in a membrane-mimicking environment (100 mM SDS aqueous solution). Furthermore, a comparison with the solution structure of full-length amyloid peptides suggests a role for the 25-27 kink region, which appears to be a general feature of all peptides under the solution conditions explored.
Literature
PMID:
15293994
Author(s):
D'Ursi, A.M., Armenante, M.R., Guerrini, R., Salvadori, S., Sorrentino, G., Picone, D.
Reference:
J Med Chem. 2004 Aug 12;47(17):4231-8
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Protein Information
Protein Name:
Amyloid-beta A4 protein
Alternative Name:
Gene Name:
Sequence Length:
11
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P05067
Keyword(s):
11-mer peptide from Amyloid beta A4 protein
Structure Information
PDB ID:
1QYT
Amyloid Category:
Amyloid
Type:
Peptide
Global Stoichiometry:
PDB Classification:
PROTEIN BINDING
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Entry:S-0059
PDB ID: 1R4C
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Sequence & Sec. Str.
Chain 1
1
G
G
P
M
D
A
S
V
E
E
E
G
V
R
R
A
L
D
F
A
V
G
E
Y
N
25
26
K
A
S
N
D
M
Y
H
S
R
A
L
Q
V
V
R
A
R
K
Q
I
V
A
G
V
50
51
N
Y
F
L
D
V
E
L
G
R
T
T
C
T
K
T
Q
P
N
L
D
N
C
P
F
75
76
H
D
Q
P
H
L
K
R
K
A
F
C
S
F
Q
I
Y
A
V
P
W
Q
G
T
M
100
101
T
L
S
K
S
T
C
Q
D
A
110
Chain 2
1
G
G
P
M
D
A
S
V
E
E
E
G
V
R
R
A
L
D
F
A
V
G
E
Y
N
25
26
K
A
S
N
D
M
Y
H
S
R
A
L
Q
V
V
R
A
R
K
Q
I
V
A
G
V
50
51
N
Y
F
L
D
V
E
L
G
R
T
T
C
T
K
T
Q
P
N
L
D
N
C
P
F
75
76
H
D
Q
P
H
L
K
R
K
A
F
C
S
F
Q
I
Y
A
V
P
W
Q
G
T
M
100
101
T
L
S
K
S
T
C
Q
D
A
110
Chain 3
1
G
G
P
M
D
A
S
V
E
E
E
G
V
R
R
A
L
D
F
A
V
G
E
Y
N
25
26
K
A
S
N
D
M
Y
H
S
R
A
L
Q
V
V
R
A
R
K
Q
I
V
A
G
V
50
51
N
Y
F
L
D
V
E
L
G
R
T
T
C
T
K
T
Q
P
N
L
D
N
C
P
F
75
76
H
D
Q
P
H
L
K
R
K
A
F
C
S
F
Q
I
Y
A
V
P
W
Q
G
T
M
100
101
T
L
S
K
S
T
C
Q
D
A
110
Chain 4
1
G
G
P
M
D
A
S
V
E
E
E
G
V
R
R
A
L
D
F
A
V
G
E
Y
N
25
26
K
A
S
N
D
M
Y
H
S
R
A
L
Q
V
V
R
A
R
K
Q
I
V
A
G
V
50
51
N
Y
F
L
D
V
E
L
G
R
T
T
C
T
K
T
Q
P
N
L
D
N
C
P
F
75
76
H
D
Q
P
H
L
K
R
K
A
F
C
S
F
Q
I
Y
A
V
P
W
Q
G
T
M
100
101
T
L
S
K
S
T
C
Q
D
A
110
Chain 5
1
G
G
P
M
D
A
S
V
E
E
E
G
V
R
R
A
L
D
F
A
V
G
E
Y
N
25
26
K
A
S
N
D
M
Y
H
S
R
A
L
Q
V
V
R
A
R
K
Q
I
V
A
G
V
50
51
N
Y
F
L
D
V
E
L
G
R
T
T
C
T
K
T
Q
P
N
L
D
N
C
P
F
75
76
H
D
Q
P
H
L
K
R
K
A
F
C
S
F
Q
I
Y
A
V
P
W
Q
G
T
M
100
101
T
L
S
K
S
T
C
Q
D
A
110
Chain 6
1
G
G
P
M
D
A
S
V
E
E
E
G
V
R
R
A
L
D
F
A
V
G
E
Y
N
25
26
K
A
S
N
D
M
Y
H
S
R
A
L
Q
V
V
R
A
R
K
Q
I
V
A
G
V
50
51
N
Y
F
L
D
V
E
L
G
R
T
T
C
T
K
T
Q
P
N
L
D
N
C
P
F
75
76
H
D
Q
P
H
L
K
R
K
A
F
C
S
F
Q
I
Y
A
V
P
W
Q
G
T
M
100
101
T
L
S
K
S
T
C
Q
D
A
110
Chain 7
1
G
G
P
M
D
A
S
V
E
E
E
G
V
R
R
A
L
D
F
A
V
G
E
Y
N
25
26
K
A
S
N
D
M
Y
H
S
R
A
L
Q
V
V
R
A
R
K
Q
I
V
A
G
V
50
51
N
Y
F
L
D
V
E
L
G
R
T
T
C
T
K
T
Q
P
N
L
D
N
C
P
F
75
76
H
D
Q
P
H
L
K
R
K
A
F
C
S
F
Q
I
Y
A
V
P
W
Q
G
T
M
100
101
T
L
S
K
S
T
C
Q
D
A
110
Chain 8
1
G
G
P
M
D
A
S
V
E
E
E
G
V
R
R
A
L
D
F
A
V
G
E
Y
N
25
26
K
A
S
N
D
M
Y
H
S
R
A
L
Q
V
V
R
A
R
K
Q
I
V
A
G
V
50
51
N
Y
F
L
D
V
E
L
G
R
T
T
C
T
K
T
Q
P
N
L
D
N
C
P
F
75
76
H
D
Q
P
H
L
K
R
K
A
F
C
S
F
Q
I
Y
A
V
P
W
Q
G
T
M
100
101
T
L
S
K
S
T
C
Q
D
A
110
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Naturally occurring Leu68Gln variant in N-truncated human cystatin C, resulting in fatal amyloidosis in early adult life
When proteins are extracted from human cystatin C amyloid deposits, an N-terminally truncated cystatin C (THCC) is found, lacking the first ten amino acid residues of the native sequence. It has been shown that the cerebrospinal fluid may cause this N-terminal truncation. The structure reveals dimerization by domain swapping. However, the new crystal structure is composed of four independent HCC dimers, none of which has the exact 2-fold symmetry of the full-length dimer. While the four dimers have the same overall topology as the full length protein.
Literature
PMID:
15312769
Author(s):
Janowski, R., Abrahamson, M., Grubb, A., Jaskolski, M.
Reference:
J Mol Biol. 2004 Jul 30;341(1):151-60
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Entry:
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Structure:
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Contact Network:
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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:
110
Species:
Homo sapiens
Mutation(s):
L68Q, 10 residue truncated fron N-terminal
E.C. Number:
UniProt ID:
P01034
Keyword(s):
Cystatin C
Structure Information
PDB ID:
1R4C
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
HYDROLASE INHIBITOR
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.18
R free:
0.259
Entry:S-0060
PDB ID: 1RVS
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Sequence & Sec. Str.
Chain 1
1
Y
T
I
A
A
L
L
S
P
Y
S
11
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
STRUCTURE OF TRANSTHYRETIN IN AMYLOID FIBRILS DETERMINED BY SOLID-STATE MAGIC ANGLE SPINNING NMR
High-resolution structure of a peptide fragment of the amyloidogenic protein transthyretin, TTR(105-115), in its fibrillar form, determined by magic angle spinning NMR spectroscopy. The structure resolves the backbone fold but also the precise conformation of the side chains. Nearly complete (13)C and (15)N resonance assignments for TTR(105-115) formed the basis for the extraction of a set of distance and dihedral angle restraints.
Literature
PMID:
14715898
Author(s):
Jaroniec, C.P., MacPhee, C.E., Bajaj, V.S., McMahon, M.T., Dobson, C.M., Griffin, R.G.
Reference:
Proc Natl Acad Sci U S A. 2004 Jan 20;101(3):711-6. Epub 2004 Jan 8
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Entry:
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JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
Gene Name:
Sequence Length:
11
Species:
Rattus norvegicus
Mutation(s):
No
E.C. Number:
UniProt ID:
P02767
Keyword(s):
Transthyretin
Structure Information
PDB ID:
1RVS
Amyloid Category:
Amyloid
Type:
FIbril
Global Stoichiometry:
PDB Classification:
DE NOVO PROTEIN
Method:
SOLID-STATE NMR
Resolution (
Å
):
R free:
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