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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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PDB ID
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Displaying 151 to 180 records out of 565 records fetched.
Entry
PDB ID
Protein
Name
Species
Length
Mutation(s)
Class
Type
Method
Resolution (
Å
)
PMID
S-0151
2NBL
Synthetic
synthetic construct
31
No
Amyloid
Fibril
SOLUTION NMR
S-0152
2NBO
Transthyretin
Homo sapiens
127
F87M/L110M
Amyloid
Protein
SOLUTION NMR
28218749
S-0153
2NBP
Transthyretin
Homo sapiens
127
T119M
Non-amyloid
Protein
SOLUTION NMR
27885756
S-0154
2NNT
Transcription elongation regulator 1
Homo sapiens
40
No
Amyloid
Fibril
SOLID-STATE NMR
17060612
S-0155
2NOY
Transthyretin
Homo sapiens
127
I84S
Non-amyloid
Protein
X-RAY DIFFRACTION
1.8
17196219
S-0156
2OCT
Cystatin-B
Homo sapiens
98
No
Amyloid
Protein
X-RAY DIFFRACTION
1.4
17217964
S-0157
2OKZ
Amyloid-beta
Homo sapiens
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.8
17468747
S-0158
2OL9
Prion protein
Homo sapiens
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
0.85
17468747
S-0159
2OLX
Yeast Prion SUP35
4
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.42
17468747
S-0160
2OMM
Eukaryotic peptide chain release factor GTP-binding subunit
Saccharomyces cerevisiae
7
No
Amyloid
Fibril
X-RAY DIFFRACTION
2.0
17468747
S-0161
2OMP
Human insulin chain A
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.9
17468747
S-0162
2OMQ
Insulin
Homo sapiens
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
2.0
17468747
S-0163
2ON9
Microtubule-associated protein tau
Homo sapiens
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.51
17468747
S-0164
2ONA
Amyloid-beta
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
2.03
17468747
S-0165
2ONV
Amyloid-beta
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.61
17468747
S-0166
2ONW
RNase A
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.51
17468747
S-0167
2ONX
Yeast prion sup35
4
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.52
17468747
S-0168
2OTK
Amyloid-beta
40 , 71 , 71
No
Non-amyloid
Inhibitor complex
SOLUTION NMR
18375754
S-0169
2Q1E
BRE
Homo sapiens
109
No
Amyloid
Protein
X-RAY DIFFRACTION
2.55
18400753
S-0170
2Q20
Immunoglobulin kappa variable 1-33
Homo sapiens
109
No
Amyloid
Protein
X-RAY DIFFRACTION
1.3
18400753
S-0171
2R0W
Amyloid-beta
223 , 219 , 8
No
Non-amyloid
Inhibitor complex
X-RAY DIFFRACTION
2.5
17895381
S-0172
2RNM
Heterokaryon incompatibility protein s
Podospora anserina
79
No
Amyloid
Fibril
SOLUTION NMR
18339938
S-0173
2TRH
Transthyretin
Homo sapiens
127
C10R
Amyloid
Protein
X-RAY DIFFRACTION
1.9
9818054
S-0174
2TRY
Transthyretin
Homo sapiens
127
S77Y
Amyloid
Protein
X-RAY DIFFRACTION
2.0
9818054
S-0175
2VB5
Beta-2-microglobulin
Homo sapiens
100
W60G
Non-amyloid
Protein
SOLUTION NMR
18395224
S-0176
2XKS
Beta-2-microglobulin
Homo sapiens
99
No
Amyloid
Protein
SOLUTION NMR
21255727
S-0177
2XKU
Beta-2-microglobulin
Homo sapiens
94
[del]N-terminal (6)
Amyloid
Protein
SOLUTION NMR
21255727
S-0178
2Y29
Amyloid-beta A4 protein
Homo sapiens
6
No
Amyloid
Peptide
X-RAY DIFFRACTION
2.3
21949245
S-0179
2Y2A
Amyloid-beta A4 protein
Homo sapiens
6
No
Amyloid
Peptide
X-RAY DIFFRACTION
1.91
21949245
S-0180
2Y3J
Amyloid-beta A4 protein
Homo sapiens
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.99
21949245
Entry:S-0151
PDB ID: 2NBL
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Structure
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Sequence & Sec. Str.
Chain 1
1
X
T
E
I
R
V
X
G
V
T
I
R
M
R
A
S
H
A
F
W
V
Q
V
P
X
25
26
K
E
F
K
H
X
31
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Peptide model of 4-stranded beta-arch; A designed peptide model of early-stage amyloid structures
A designed peptide model of early-stage amyloid structures
Literature
PMID:
Author(s):
Kung, V.
Reference:
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
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JSON
Protein Information
Protein Name:
Synthetic
Alternative Name:
Gene Name:
Sequence Length:
31
Species:
synthetic construct
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Designed beta-arch
Structure Information
PDB ID:
2NBL
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Monomer - A
PDB Classification:
DE NOVO PROTEIN
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
4FU
A
C8 H12 O4
172.18
(1R,2S)-cyclohexane-1,2-dicarboxylic acid
C1CC[C@@H]([C@@H](C1)C(=O)O)C(=O)O
QSAWQNUELGIYBC-OLQVQODUSA-N
4G6
A
C4 H12 N2
88.15
2-methylpropane-1,2-diamine
CC(C)(CN)N
OPCJOXGBLDJWRM-UHFFFAOYSA-N
ACE
A
C2 H4 O
44.05
ACETYL GROUP
CC=O
IKHGUXGNUITLKF-UHFFFAOYSA-N
DAL
A
C3 H7 N O2
89.09
D-ALANINE
C[C@H](C(=O)O)N
QNAYBMKLOCPYGJ-UWTATZPHSA-N
DPR
A
C5 H9 N O2
115.13
D-PROLINE
C1C[C@@H](NC1)C(=O)O
ONIBWKKTOPOVIA-SCSAIBSYSA-N
NH2
A
H2 N
16.02
AMINO GROUP
[NH2]
QGZKDVFQNNGYKY-UHFFFAOYAF
Entry:S-0152
PDB ID: 2NBO
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Structure
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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
M
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
M
L
S
P
Y
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
Solution structure of the F87M/L110M variant of transthyretin in the monomeric state; misfolded cytotoxic monomer
They used nuclear magnetic resonance (NMR) spectroscopy to determine the three-dimensional structure of the misfolded cytotoxic monomer of the amyloidogenic human protein transthyretin, which is characterized by the release of the C-terminal Beta-strand and perturbations of the A-B loop. The misfolded transthyretin monomer, but not the wild-type protein, binds to human Hsp90. In the bound state, the Hsp90 dimer predominantly populates an open conformation, and transthyretin retains its globular structure. The interaction surface for the transthyretin monomer comprises the N-terminal and middle domains of Hsp90 and overlaps with that of the Alzheimer's-disease-related protein tau.
Literature
PMID:
28218749
Author(s):
Oroz, J., Kim, J.H., Chang, B.J., Zweckstetter, M.
Reference:
Nat Struct Mol Biol. 2017 Apr;24(4):407-413.
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Entry:
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JSON
Structure:
PDB
CIF
FASTA
Contact Network:
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JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
127
Species:
Homo sapiens
Mutation(s):
F87M/L110M
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
2NBO
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
TRANSPORT PROTEIN
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Entry:S-0153
PDB ID: 2NBP
CSV
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Structure
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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
M
H
E
H
A
E
V
V
F
T
A
N
D
S
100
101
G
P
R
R
Y
T
I
A
A
M
L
S
P
Y
S
Y
S
T
M
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
Structure of Monomeric Transthyretin Carrying the Clinically Important T119M Mutation
They determined the solution structure of a transthyretin monomer that carries the clinically important T119M mutation. The structure displays a non-native arrangement that is distinct from all known structures of transthyretin and highlights the importance of high-resolution studies in solution for understanding molecular processes that lead to amyloid diseases. A TTR mutation T119M has a high frequency of occurrence in the Portuguese population and it protects heterozygous individuals from TTR amyloid disease.
Literature
PMID:
27885756
Author(s):
Kim, J.H., Oroz, J., Zweckstetter, M.
Reference:
Angew Chem Int Ed Engl. 2016 Dec 23;55(52):16168-16171.
Download
Entry:
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Structure:
PDB
CIF
FASTA
Contact Network:
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JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
127
Species:
Homo sapiens
Mutation(s):
T119M
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
2NBP
Amyloid Category:
Non-amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
TRANSPORT PROTEIN
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Entry:S-0154
PDB ID: 2NNT
CSV
JSON
Close ×
Structure
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Sequence & Sec. Str.
Chain 1
1
G
S
M
G
A
T
A
V
S
E
W
T
E
Y
K
T
A
D
G
K
T
F
Y
Y
N
25
26
N
R
T
L
E
S
T
W
E
K
P
Q
E
L
K
40
Chain 2
1
G
S
M
G
A
T
A
V
S
E
W
T
E
Y
K
T
A
D
G
K
T
F
Y
Y
N
25
26
N
R
T
L
E
S
T
W
E
K
P
Q
E
L
K
40
Chain 3
1
G
S
M
G
A
T
A
V
S
E
W
T
E
Y
K
T
A
D
G
K
T
F
Y
Y
N
25
26
N
R
T
L
E
S
T
W
E
K
P
Q
E
L
K
40
Chain 4
1
G
S
M
G
A
T
A
V
S
E
W
T
E
Y
K
T
A
D
G
K
T
F
Y
Y
N
25
26
N
R
T
L
E
S
T
W
E
K
P
Q
E
L
K
40
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
General structural motifs of amyloid protofilaments
"Human CA150, a transcriptional activator, binds to and is co-deposited with huntingtin during Huntington's disease. The second WW domain of CA150 is a three-stranded Beta-sheet that folds in vitro in microseconds and forms amyloid fibers under physiological conditions. The structure has similarities to the hairpin formed by the A(Beta)((1-40)) protofilament, yet also contains closely packed side-chains in a ""steric zipper"" arrangement found in the cross-Beta spine formed from small peptides from the Sup35 prion protein. "
Literature
PMID:
17060612
Author(s):
Ferguson, N., Becker, J., Tidow, H., Tremmel, S., Sharpe, T.D., Krause, G., Flinders, J., Petrovich, M., Berriman, J., Oschkinat, H., Fersht, A.R.
Reference:
Proc Natl Acad Sci U S A. 2006 Oct 31;103(44):16248-53. Epub 2006 Oct 23
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Entry:
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Structure:
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Protein Information
Protein Name:
Transcription elongation regulator 1
Alternative Name:
TATA box-binding protein-associated factor 2S, Transcription factor CA150
Gene Name:
TCERG1, CA150, TAF2S
Sequence Length:
40
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
O14776
Keyword(s):
Transcription elongation regulator 1
Structure Information
PDB ID:
2NNT
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
PROTEIN FIBRIL
Method:
SOLID-STATE NMR
Resolution (
Å
):
R free:
Entry:S-0155
PDB ID: 2NOY
CSV
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Close ×
Structure
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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
S
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
Y
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
S
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
Y
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
In vitro, the natural amyloidogenic I84S mutant form exhibit a propensity to produce fibrils in an acidic medium significantly higher than that of wild-type TTR
In vitro, the natural amyloidogenic I84S and the non-natural I84A TTR mutant forms exhibit a propensity to produce fibrils in an acidic medium significantly higher than that of wild-type TTR. The two mutant forms have been crystallized at both neutral and acidic pH. Their neutral pH crystal structures are very similar to that of wild-type TTR, consistent with previous evidence indicating that only minor structural changes are induced by amyloidogenic mutations. On the contrary, their crystal structures at moderately low pH (4.6) show significant conformational differences as compared to their neutral pH structures. Remarkably, such changes are not induced in wild-type TTR crystallized at low pH. The most relevant consist of the unwinding of the TTR short Alpha-helix and of the change in conformation of the loop connecting the Alpha-helix to Beta-strand F. Only one monomer of the crystallographic dimer is affected, causing a disruption of the tetrameric symmetry. This asymmetry and a possible destabilization of the tetrameric quaternary structure of TTR may be responsible for the amyloidogenic potential of the two TTR mutant forms at low pH.
Literature
PMID:
17196219
Author(s):
Pasquato, N., Berni, R., Folli, C., Alfieri, B., Cendron, L., Zanotti, G.
Reference:
J Mol Biol. 2007 Feb 23;366(3):711-9. Epub 2006 Dec 1
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Entry:
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Structure:
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CIF
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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):
I84S
E.C. Number:
UniProt ID:
P02766
Keyword(s):
Transthyretin
Structure Information
PDB ID:
2NOY
Amyloid Category:
Non-amyloid
Type:
Protein
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
TRANSPORT PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.8
R free:
0.251
Entry:S-0156
PDB ID: 2OCT
CSV
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Close ×
Structure
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View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
M
M
S
G
A
P
S
A
T
Q
P
A
T
A
E
T
Q
H
I
A
D
Q
V
R
S
25
26
Q
L
E
E
K
Y
N
K
K
F
P
V
F
K
A
V
S
F
K
S
Q
V
V
A
G
50
51
T
N
Y
F
I
K
V
H
V
G
D
E
D
F
V
H
L
R
V
F
Q
S
L
P
H
75
76
E
N
K
S
L
T
L
S
N
Y
Q
T
N
K
A
K
H
D
E
L
T
Y
F
98
Chain 2
1
M
M
S
G
A
P
S
A
T
Q
P
A
T
A
E
T
Q
H
I
A
D
Q
V
R
S
25
26
Q
L
E
E
K
Y
N
K
K
F
P
V
F
K
A
V
S
F
K
S
Q
V
V
A
G
50
51
T
N
Y
F
I
K
V
H
V
G
D
E
D
F
V
H
L
R
V
F
Q
S
L
P
H
75
76
E
N
K
S
L
T
L
S
N
Y
Q
T
N
K
A
K
H
D
E
L
T
Y
F
98
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Stefin B (Cystatin B) tetramer
The tetrameric structure of stefin B is the result of a process by which two domain-swapped dimers of stefin B are transformed into tetramers. The transformation involves a previously unidentified process of extensive intermolecular contacts, termed hand shaking, which occurs concurrently with trans to cis isomerization of proline 74. This proline residue is widely conserved throughout the cystatin superfamily, a member of which, human cystatin C, is the key protein in cerebral amyloid angiopathy. These results are consistent with the hypothesis that isomerization of proline residues can play a decisive role in amyloidogenesis.
Literature
PMID:
17217964
Author(s):
Jenko Kokalj, S., Guncar, G., Stern, I., Morgan, G., Rabzelj, S., Kenig, M., Staniforth, R.A., Waltho, J.P., Zerovnik, E., Turk, D.
Reference:
J Mol Biol. 2007 Mar 9;366(5):1569-79. Epub 2006 Dec 16
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Protein Information
Protein Name:
Cystatin-B
Alternative Name:
CPI-B, Liver thiol proteinase inhibitor, Stefin-B
Gene Name:
CSTB, CST6, STFB
Sequence Length:
98
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P04080
Keyword(s):
Cystatin B
Structure Information
PDB ID:
2OCT
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
PROTEIN BINDING
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.4
R free:
0.18899999
Entry:S-0157
PDB ID: 2OKZ
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Sequence & Sec. Str.
Chain 1
1
M
V
G
G
V
V
6
Chain 2
1
M
V
G
G
V
V
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
MVGGVV peptide derived from Alzheimer's A-beta
Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-Beta spine. Structures of microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains.
Literature
PMID:
17468747
Author(s):
Sawaya, M.R., Sambashivan, S., Nelson, R., Ivanova, M.I., Sievers, S.A., Apostol, M.I., Thompson, M.J., Balbirnie, M., Wiltzius, J.J., McFarlane, H.T., Madsen, A.O., Riekel, C., Eisenberg, D.
Reference:
Nature. 2007 May 24;447(7143):453-7. Epub 2007 Apr 29
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Protein Information
Protein Name:
Amyloid-beta
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
peptide from Alzheimer's A-beta
Structure Information
PDB ID:
2OKZ
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:
0.267
Entry:S-0158
PDB ID: 2OL9
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Sequence & Sec. Str.
Chain 1
1
S
N
Q
N
N
F
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Peptide corresponding to residues 170-175 of human prion
Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-Beta spine. Structures of microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains.
Literature
PMID:
17468747
Author(s):
Sawaya, M.R., Sambashivan, S., Nelson, R., Ivanova, M.I., Sievers, S.A., Apostol, M.I., Thompson, M.J., Balbirnie, M., Wiltzius, J.J., McFarlane, H.T., Madsen, A.O., Riekel, C., Eisenberg, D.
Reference:
Nature. 2007 May 24;447(7143):453-7. Epub 2007 Apr 29
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Protein Information
Protein Name:
Prion protein
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
peptide from human prion
Structure Information
PDB ID:
2OL9
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
0.85
R free:
0.078
Entry:S-0159
PDB ID: 2OLX
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Sequence & Sec. Str.
Chain 1
1
N
N
Q
Q
4
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Structure of NNQQ Peptide from Yeast Prion SUP35
Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-Beta spine. Structures of microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains.
Literature
PMID:
17468747
Author(s):
Sawaya, M.R., Sambashivan, S., Nelson, R., Ivanova, M.I., Sievers, S.A., Apostol, M.I., Thompson, M.J., Balbirnie, M., Wiltzius, J.J., McFarlane, H.T., Madsen, A.O., Riekel, C., Eisenberg, D.
Reference:
Nature. 2007 May 24;447(7143):453-7. Epub 2007 Apr 29
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Protein Information
Protein Name:
Yeast Prion SUP35
Alternative Name:
Gene Name:
Sequence Length:
4
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
NNQQ peptide derived from Yeast Prion Sup35
Structure Information
PDB ID:
2OLX
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.42
R free:
0.235
Entry:S-0160
PDB ID: 2OMM
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Sequence & Sec. Str.
Chain 1
1
G
N
N
Q
Q
N
Y
7
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
GNNQQNY peptide corresponding to residues 7-13 of yeast prion sup35
Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-Beta spine. Structures of microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains.
Literature
PMID:
17468747
Author(s):
Sawaya, M.R., Sambashivan, S., Nelson, R., Ivanova, M.I., Sievers, S.A., Apostol, M.I., Thompson, M.J., Balbirnie, M., Wiltzius, J.J., McFarlane, H.T., Madsen, A.O., Riekel, C., Eisenberg, D.
Reference:
Nature. 2007 May 24;447(7143):453-7. Epub 2007 Apr 29
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Protein Information
Protein Name:
Eukaryotic peptide chain release factor GTP-binding subunit
Alternative Name:
Gene Name:
Sequence Length:
7
Species:
Saccharomyces cerevisiae
Mutation(s):
No
E.C. Number:
UniProt ID:
P05453
Keyword(s):
GNNQQNY peptide corresponding to residues 7-13 of yeast prion sup35
Structure Information
PDB ID:
2OMM
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.0
R free:
0.252
Entry:S-0161
PDB ID: 2OMP
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Sequence & Sec. Str.
Chain 1
1
L
Y
Q
L
E
N
6
Chain 2
1
L
Y
Q
L
E
N
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
LYQLEN peptide derived from human insulin chain A, residues 13-18
Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-Beta spine. Structures of microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains.
Literature
PMID:
17468747
Author(s):
Sawaya, M.R., Sambashivan, S., Nelson, R., Ivanova, M.I., Sievers, S.A., Apostol, M.I., Thompson, M.J., Balbirnie, M., Wiltzius, J.J., McFarlane, H.T., Madsen, A.O., Riekel, C., Eisenberg, D.
Reference:
Nature. 2007 May 24;447(7143):453-7. Epub 2007 Apr 29
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Protein Information
Protein Name:
Human insulin chain A
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
LYQLEN peptide derived from human insulin chain A, residues 13-18
Structure Information
PDB ID:
2OMP
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 8-mer - A8
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.9
R free:
0.228
Entry:S-0162
PDB ID: 2OMQ
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Sequence & Sec. Str.
Chain 1
1
V
E
A
L
Y
L
6
Chain 2
1
V
E
A
L
Y
L
6
Chain 3
1
V
E
A
L
Y
L
6
Chain 4
1
V
E
A
L
Y
L
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
VEALYL peptide derived from human insulin chain B, residues 12-17
Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-Beta spine. Structures of microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains.
Literature
PMID:
17468747
Author(s):
Sawaya, M.R., Sambashivan, S., Nelson, R., Ivanova, M.I., Sievers, S.A., Apostol, M.I., Thompson, M.J., Balbirnie, M., Wiltzius, J.J., McFarlane, H.T., Madsen, A., Riekel, C., Eisenberg, D.
Reference:
Nature. 2007 May 24;447(7143):453-7. Epub 2007 Apr 29
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Protein Information
Protein Name:
Insulin
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P01308
Keyword(s):
VEALYL peptide derived from human insulin chain B, residues 12-17
Structure Information
PDB ID:
2OMQ
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 8-mer - A8
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.0
R free:
0.265
Entry:S-0163
PDB ID: 2ON9
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Sequence & Sec. Str.
Chain 1
1
V
Q
I
V
Y
K
6
Chain 2
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 repeat region of Tau
Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-Beta spine. Structures of microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains.
Literature
PMID:
17468747
Author(s):
Sawaya, M.R., Sambashivan, S., Nelson, R., Ivanova, M.I., Sievers, S.A., Apostol, M.I., Thompson, M.J., Balbirnie, M., Wiltzius, J.J., McFarlane, H.T., Madsen, A.O., Riekel, C., Eisenberg, D.
Reference:
Nature. 2007 May 24;447(7143):453-7. Epub 2007 Apr 29
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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):
VQIVYK peptide corresponding to residues 306-311 in the tau protein
Structure Information
PDB ID:
2ON9
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.51
R free:
0.225
Entry:S-0164
PDB ID: 2ONA
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Sequence & Sec. Str.
Chain 1
1
M
V
G
G
V
V
6
Chain 2
1
M
V
G
G
V
V
6
Chain 3
1
M
V
G
G
V
V
6
Chain 4
1
M
V
G
G
V
V
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40
Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-Beta spine. Structures of microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains.
Literature
PMID:
17468747
Author(s):
Sawaya, M.R., Sambashivan, S., Nelson, R., Ivanova, M.I., Sievers, S.A., Apostol, M.I., Thompson, M.J., Balbirnie, M., Wiltzius, J.J., McFarlane, H.T., Madsen, A.O., Riekel, C., Eisenberg, D.
Reference:
Nature. 2007 May 24;447(7143):453-7. Epub 2007 Apr 29
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Entry:
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Protein Information
Protein Name:
Amyloid-beta
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40
Structure Information
PDB ID:
2ONA
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 8-mer - A8
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.03
R free:
0.264
Entry:S-0165
PDB ID: 2ONV
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Sequence & Sec. Str.
Chain 1
1
G
G
V
V
I
A
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal Structure of the amyloid-fibril forming peptide GGVVIA derived from the Alzheimer's amyloid Abeta (Abeta37-42).
Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-Beta spine. Structures of microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains.
Literature
PMID:
17468747
Author(s):
Sawaya, M.R., Sambashivan, S., Nelson, R., Ivanova, M.I., Sievers, S.A., Apostol, M.I., Thompson, M.J., Balbirnie, M., Wiltzius, J.J., McFarlane, H.T., Madsen, A.O., Riekel, C., Eisenberg, D.
Reference:
Nature. 2007 May 24;447(7143):453-7. Epub 2007 Apr 29
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Entry:
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Structure:
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Protein Information
Protein Name:
Amyloid-beta
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
amyloid-fibril forming peptide GGVVIA derived from the Alzheimer's amyloid Abeta
Structure Information
PDB ID:
2ONV
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.61
R free:
0.299
Entry:S-0166
PDB ID: 2ONW
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Sequence & Sec. Str.
Chain 1
1
S
S
T
S
A
A
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Structure of SSTSSA, a fibril forming peptide from Bovine Pancreatic Ribonuclease (RNase A, residues 15-20)
Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-Beta spine. Structures of microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains.
Literature
PMID:
17468747
Author(s):
Sawaya, M.R., Sambashivan, S., Nelson, R., Ivanova, M.I., Sievers, S.A., Apostol, M.I., Thompson, M.J., Balbirnie, M., Wiltzius, J.J., McFarlane, H.T., Madsen, A.O., Riekel, C., Eisenberg, D.
Reference:
Nature. 2007 May 24;447(7143):453-7. Epub 2007 Apr 29
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Entry:
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Protein Information
Protein Name:
RNase A
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
fibril forming peptide from Bovine Pancreatic Ribonuclease (RNase A)
Structure Information
PDB ID:
2ONW
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.51
R free:
0.21899999
Entry:S-0167
PDB ID: 2ONX
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Sequence & Sec. Str.
Chain 1
1
N
N
Q
Q
4
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
NNQQ peptide corresponding to residues 8-11 of yeast prion sup35 (alternate crystal form)
Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-Beta spine. Structures of microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains.
Literature
PMID:
17468747
Author(s):
Sawaya, M.R., Sambashivan, S., Nelson, R., Ivanova, M.I., Sievers, S.A., Apostol, M.I., Thompson, M.J., Balbirnie, M., Wiltzius, J.J., McFarlane, H.T., Madsen, A.O., Riekel, C., Eisenberg, D.
Reference:
Nature. 2007 May 24;447(7143):453-7. Epub 2007 Apr 29
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Entry:
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Structure:
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Protein Information
Protein Name:
Yeast prion sup35
Alternative Name:
Gene Name:
Sequence Length:
4
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
peptide corresponding to residues 8-11 of yeast prion sup35
Structure Information
PDB ID:
2ONX
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.52
R free:
0.20199999
Entry:S-0168
PDB ID: 2OTK
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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
40
Chain 2
1
G
S
S
H
H
H
H
H
H
L
Q
V
D
N
K
F
N
K
E
M
A
S
A
G
G
25
26
E
I
V
Y
L
P
N
L
N
P
D
Q
L
C
A
F
I
H
S
L
H
D
D
P
S
50
51
Q
S
A
N
L
L
A
E
A
K
K
L
N
D
A
Q
A
P
K
V
D
71
Chain 3
1
G
S
S
H
H
H
H
H
H
L
Q
V
D
N
K
F
N
K
E
M
A
S
A
G
G
25
26
E
I
V
Y
L
P
N
L
N
P
D
Q
L
C
A
F
I
H
S
L
H
D
D
P
S
50
51
Q
S
A
N
L
L
A
E
A
K
K
L
N
D
A
Q
A
P
K
V
D
71
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Structure of Alzheimer Ab peptide in complex with an engineered binding protein; Stabilization of a beta-hairpin in monomeric Alzheimer's amyloid-beta peptide inhibits amyloid formation.
The solution structure of ABeta(1-40) in complex with the phage-display selected affibody protein Z(ABeta3), a binding protein of nanomolar affinity. Bound ABeta(1-40) features a Beta-hairpin comprising residues 17-36, providing the first high-resolution structure of ABeta in Beta conformation. The positions of the secondary structure elements strongly resemble those observed for fibrillar ABeta. Z(ABeta3) stabilizes the Beta-sheet by extending it intermolecularly and by burying both of the mostly nonpolar faces of the ABeta hairpin within a large hydrophobic tunnel-like cavity. Consequently, Z(ABeta3) acts as a stoichiometric inhibitor of ABeta fibrillation.
Literature
PMID:
18375754
Author(s):
Hoyer, W., Gronwall, C., Jonsson, A., Stahl, S., Hard, T.
Reference:
Proc Natl Acad Sci U S A. 2008 Apr 1;105(13):5099-104.
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Structure:
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Protein Information
Protein Name:
Amyloid-beta
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:
40 , 71 , 71
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Structure Information
PDB ID:
2OTK
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Hetero 3-mer - A2B
PDB Classification:
DE NOVO PROTEIN
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Entry:S-0169
PDB ID: 2Q1E
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JSON
Close ×
Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
A
T
D
I
Q
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
25
26
Q
A
S
Q
D
I
N
N
Y
L
I
W
Y
Q
Q
K
P
G
Q
A
P
K
L
L
I
50
51
Y
D
A
S
T
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
E
F
T
F
75
76
T
I
S
S
L
Q
P
E
D
L
A
T
Y
H
C
Q
Q
Y
D
N
L
P
Y
T
F
100
101
G
Q
G
T
K
L
E
I
K
109
Chain 2
1
A
T
D
I
Q
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
25
26
Q
A
S
Q
D
I
N
N
Y
L
I
W
Y
Q
Q
K
P
G
Q
A
P
K
L
L
I
50
51
Y
D
A
S
T
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
E
F
T
F
75
76
T
I
S
S
L
Q
P
E
D
L
A
T
Y
H
C
Q
Q
Y
D
N
L
P
Y
T
F
100
101
G
Q
G
T
K
L
E
I
K
109
Chain 3
1
A
T
D
I
Q
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
25
26
Q
A
S
Q
D
I
N
N
Y
L
I
W
Y
Q
Q
K
P
G
Q
A
P
K
L
L
I
50
51
Y
D
A
S
T
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
E
F
T
F
75
76
T
I
S
S
L
Q
P
E
D
L
A
T
Y
H
C
Q
Q
Y
D
N
L
P
Y
T
F
100
101
G
Q
G
T
K
L
E
I
K
109
Chain 4
1
A
T
D
I
Q
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
25
26
Q
A
S
Q
D
I
N
N
Y
L
I
W
Y
Q
Q
K
P
G
Q
A
P
K
L
L
I
50
51
Y
D
A
S
T
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
E
F
T
F
75
76
T
I
S
S
L
Q
P
E
D
L
A
T
Y
H
C
Q
Q
Y
D
N
L
P
Y
T
F
100
101
G
Q
G
T
K
L
E
I
K
109
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Altered dimer interface decreases stability in an amyloidogenic kappa1 Bence Jones protein. AL-09
AL-09 has an altered dimer interface that is rotated 90 degrees from the kappaI O18/O8 dimer interface. The three non-conservative mutations in AL-09 are located within the dimer interface, consistent with their role in the decreased stability of this amyloidogenic protein.
Literature
PMID:
18400753
Author(s):
Baden, E.M., Owen, B.A., Peterson, F.C., Volkman, B.F., Ramirez-Alvarado, M., Thompson, J.R.
Reference:
J Biol Chem. 2008 Jun 6;283(23):15853-60.
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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:
BRE
Alternative Name:
Gene Name:
Sequence Length:
109
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
A2NI60
Keyword(s):
Amyloidogenic immunoglobulin light chain protein AL-09
Structure Information
PDB ID:
2Q1E
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.55
R free:
0.20600000
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
Entry:S-0170
PDB ID: 2Q20
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
S
T
D
I
Q
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
25
26
Q
A
S
Q
D
I
S
N
Y
L
N
W
Y
Q
Q
K
P
G
K
A
P
K
L
L
I
50
51
Y
D
A
S
N
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
D
F
T
F
75
76
T
I
S
S
L
Q
P
E
D
I
A
T
Y
Y
C
Q
Q
Y
D
N
L
P
Y
T
F
100
101
G
Q
G
T
K
L
E
I
K
109
Chain 2
1
S
T
D
I
Q
M
T
Q
S
P
S
S
L
S
A
S
V
G
D
R
V
T
I
T
C
25
26
Q
A
S
Q
D
I
S
N
Y
L
N
W
Y
Q
Q
K
P
G
K
A
P
K
L
L
I
50
51
Y
D
A
S
N
L
E
T
G
V
P
S
R
F
S
G
S
G
S
G
T
D
F
T
F
75
76
T
I
S
S
L
Q
P
E
D
I
A
T
Y
Y
C
Q
Q
Y
D
N
L
P
Y
T
F
100
101
G
Q
G
T
K
L
E
I
K
109
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Structure of the germline Vk1 O18/O8 light chain variable domain homodimer
They have compare light chain amyloidosis protein AL-09 to its wild-type counterpart, the kappaI O18/O8 light chain germline. AL-09 (PDB ID 2Q1E) forms amyloid fibrils more quickly than kappaI O18/O8 in vitro.
Literature
PMID:
18400753
Author(s):
Baden, E.M., Owen, B.A., Peterson, F.C., Volkman, B.F., Ramirez-Alvarado, M., Thompson, J.R.
Reference:
J Biol Chem. 2008 Jun 6;283(23):15853-60.
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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:
109
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P01594
Keyword(s):
Vk1 O18/O8 germline light chain variable domain
Structure Information
PDB ID:
2Q20
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 2-mer - A2
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.3
R free:
0.14800000
Entry:S-0171
PDB ID: 2R0W
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Close ×
Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
Q
V
T
L
K
E
S
G
P
G
I
L
K
P
S
Q
T
L
S
L
T
C
S
L
S
25
26
G
F
S
L
R
T
S
G
M
G
V
G
W
I
R
Q
P
S
G
K
G
L
E
W
L
50
51
A
H
I
W
W
D
D
D
K
N
Y
N
P
S
L
K
S
Q
L
T
I
S
K
D
T
75
76
S
R
N
Q
V
F
L
K
I
T
S
V
D
T
A
D
T
A
T
Y
Y
C
V
R
R
100
101
A
H
N
V
V
L
G
D
W
F
A
Y
W
G
Q
G
T
L
V
T
V
S
A
A
K
125
126
T
T
A
P
S
V
Y
P
L
A
P
V
C
G
D
T
T
G
S
S
V
T
L
G
C
150
151
L
V
K
G
Y
F
P
E
P
V
T
L
T
W
N
S
G
S
L
S
S
G
V
H
T
175
176
F
P
A
V
L
Q
S
D
L
Y
T
L
S
S
S
V
T
V
T
S
S
T
W
P
S
200
201
Q
S
I
T
C
N
V
A
H
P
A
S
S
T
K
V
D
K
K
I
E
P
R
223
Chain 2
1
D
V
L
M
T
Q
T
P
L
S
L
P
V
S
L
G
D
Q
A
S
I
S
C
R
S
25
26
S
Q
S
I
V
H
S
N
G
N
T
Y
L
E
W
Y
L
Q
K
P
G
Q
S
P
K
50
51
L
L
I
Y
K
V
S
N
R
F
S
G
V
P
D
R
F
S
G
S
G
S
G
T
D
75
76
F
T
L
K
I
S
R
V
E
A
E
D
L
G
V
Y
Y
C
F
Q
G
S
H
V
P
100
101
L
T
F
G
A
G
T
K
L
E
I
K
R
A
D
A
A
P
T
V
S
I
F
P
P
125
126
S
S
E
Q
L
T
S
G
G
A
S
V
V
C
F
L
N
N
F
Y
P
K
D
I
N
150
151
V
K
W
K
I
D
G
S
E
R
Q
N
G
V
L
N
S
W
T
D
Q
D
S
K
D
175
176
S
T
Y
S
M
S
S
T
L
T
L
T
K
D
E
Y
E
R
H
N
S
Y
T
C
E
200
201
A
T
H
K
T
S
T
S
P
I
V
K
S
F
N
R
N
E
C
219
Chain 3
1
D
A
E
F
R
H
D
S
8
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
PFA2 FAB complexed with Abeta1-8
The structures of antigen binding fragments (Fabs) in complex with the ABeta(1-8) peptide DAEFRHDS. The immunodominant EFRHD sequence forms salt bridges, hydrogen bonds, and hydrophobic contacts, including interactions with a striking WWDDD motif of the antigen binding fragments.
Literature
PMID:
17895381
Author(s):
Gardberg, A.S., Dice, L.T., Ou, S., Rich, R.L., Helmbrecht, E., Ko, J., Wetzel, R., Myszka, D.G., Patterson, P.H., Dealwis, C.
Reference:
Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15659-64. Epub 2007 Sep 25
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Structure:
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Protein Information
Protein Name:
Amyloid-beta
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:
Igkc, Igk-C & APP, A4, AD1
Sequence Length:
223 , 219 , 8
Species:
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
Structure Information
PDB ID:
2R0W
Amyloid Category:
Non-amyloid
Type:
Inhibitor complex
Global Stoichiometry:
Homo 2-mer -A2
PDB Classification:
IMMUNE SYSTEM
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.5
R free:
0.27699999
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
nan
L
Na 1
22.99
SODIUM ION
[Na+]
FKNQFGJONOIPTF-UHFFFAOYSA-N
YCM
L
C5 H10 N2 O3 S
178.21
S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE
C([C@@H](C(=O)O)N)SCC(=O)N
VFKYKPOTSJWPIU-VKHMYHEASA-N
Entry:S-0172
PDB ID: 2RNM
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Close ×
Structure
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Sequence & Sec. Str.
Chain 1
1
M
K
I
D
A
I
V
G
R
N
S
A
K
D
I
R
T
E
E
R
A
R
V
Q
L
25
26
G
N
V
V
T
A
A
A
L
H
G
G
I
R
I
S
D
Q
T
T
N
S
V
E
T
50
51
V
V
G
K
G
E
S
R
V
L
I
G
N
E
Y
G
G
K
G
F
W
D
N
H
H
75
76
H
H
H
H
79
Chain 2
1
M
K
I
D
A
I
V
G
R
N
S
A
K
D
I
R
T
E
E
R
A
R
V
Q
L
25
26
G
N
V
V
T
A
A
A
L
H
G
G
I
R
I
S
D
Q
T
T
N
S
V
E
T
50
51
V
V
G
K
G
E
S
R
V
L
I
G
N
E
Y
G
G
K
G
F
W
D
N
H
H
75
76
H
H
H
H
79
Chain 3
1
M
K
I
D
A
I
V
G
R
N
S
A
K
D
I
R
T
E
E
R
A
R
V
Q
L
25
26
G
N
V
V
T
A
A
A
L
H
G
G
I
R
I
S
D
Q
T
T
N
S
V
E
T
50
51
V
V
G
K
G
E
S
R
V
L
I
G
N
E
Y
G
G
K
G
F
W
D
N
H
H
75
76
H
H
H
H
79
Chain 4
1
M
K
I
D
A
I
V
G
R
N
S
A
K
D
I
R
T
E
E
R
A
R
V
Q
L
25
26
G
N
V
V
T
A
A
A
L
H
G
G
I
R
I
S
D
Q
T
T
N
S
V
E
T
50
51
V
V
G
K
G
E
S
R
V
L
I
G
N
E
Y
G
G
K
G
F
W
D
N
H
H
75
76
H
H
H
H
79
Chain 5
1
M
K
I
D
A
I
V
G
R
N
S
A
K
D
I
R
T
E
E
R
A
R
V
Q
L
25
26
G
N
V
V
T
A
A
A
L
H
G
G
I
R
I
S
D
Q
T
T
N
S
V
E
T
50
51
V
V
G
K
G
E
S
R
V
L
I
G
N
E
Y
G
G
K
G
F
W
D
N
H
H
75
76
H
H
H
H
79
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Structure of The HET-s(218-289) prion in its amyloid form obtained by solid-state NMR
A structural model for amyloid fibrils from the prion-forming domain (residues 218 to 289) of the HET-s protein from the filamentous fungus Podospora anserina. HET-s(218-289) forms a left-handed Beta solenoid, with each molecule forming two helical windings, a compact hydrophobic core, at least 23 hydrogen bonds, three salt bridges, and two asparagine ladders.
Literature
PMID:
18339938
Author(s):
Wasmer, C., Lange, A., Van Melckebeke, H., Siemer, A.B., Riek, R., Meier, B.H.
Reference:
Science. 2008 Mar 14;319(5869):1523-6.
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Structure:
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Protein Information
Protein Name:
Heterokaryon incompatibility protein s
Alternative Name:
Small s protein, Vegetative incompatibility protein s
Gene Name:
het-s, small s
Sequence Length:
79
Species:
Podospora anserina
Mutation(s):
No
E.C. Number:
UniProt ID:
Q03689
Keyword(s):
Small s protein
Structure Information
PDB ID:
2RNM
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 5-mer - A5
PDB Classification:
PROTEIN FIBRIL
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Entry:S-0173
PDB ID: 2TRH
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
P
T
G
T
G
E
S
K
R
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
Y
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
R
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
Y
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
Tertiary structures of amyloidogenic and non-amyloidogenic transthyretin variants
They reported crystallization and structural investigations of three amyloidogenic (Arg10, Ala60, Tyr77) and two non-amyloidogenic variants (Ser6, Met119). The similarity of these structures to normal transthyretin does not give direct clues to the fibril forming process. All amyloidogenic variants show an increased main chain solvent exposure when compared to normal transthyretin and non-amyloidogenic variants, which can be postulated to result in increased susceptibility to proteolysis.
Literature
PMID:
9818054
Author(s):
Schormann, N., Murrell, J.R., Benson, M.D.
Reference:
Amyloid. 1998 Sep;5(3):175-87
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Entry:
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Structure:
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FASTA
Contact Network:
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JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
ATTR, Prealbumin, TBPA
Gene Name:
TTR, PALB
Sequence Length:
127
Species:
Homo sapiens
Mutation(s):
C10R
E.C. Number:
UniProt ID:
P02766
Keyword(s):
TRANSTHYRETIN
Structure Information
PDB ID:
2TRH
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
TRANSPORT
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.9
R free:
0.299
Entry:S-0174
PDB ID: 2TRY
CSV
JSON
Close ×
Structure
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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
Y
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
Y
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
Y
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
Y
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
Tertiary structures of amyloidogenic and non-amyloidogenic transthyretin variants
They reported crystallization and structural investigations of three amyloidogenic (Arg10, Ala60, Tyr77) and two non-amyloidogenic variants (Ser6, Met119). The similarity of these structures to normal transthyretin does not give direct clues to the fibril forming process. All amyloidogenic variants show an increased main chain solvent exposure when compared to normal transthyretin and non-amyloidogenic variants, which can be postulated to result in increased susceptibility to proteolysis.
Literature
PMID:
9818054
Author(s):
Schormann, N., Murrell, J.R., Benson, M.D.
Reference:
Amyloid. 1998 Sep;5(3):175-87
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:
127
Species:
Homo sapiens
Mutation(s):
S77Y
E.C. Number:
UniProt ID:
P02766
Keyword(s):
TRANSTHYRETIN
Structure Information
PDB ID:
2TRY
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
TRANSPORT
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.0
R free:
0.31
Entry:S-0175
PDB ID: 2VB5
CSV
JSON
Close ×
Structure
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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
G
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
Solution structure of W60G mutant of human beta2-microglobulin
The Trp60-->Gly mutation has a threefold effect on Beta(2)m: it stabilizes Beta(2)m, inhibits Beta(2)m amyloidogenic propensity and weakens the interaction with the class I major histocompatibility complex heavy chain. Solution NMR structure.
Literature
PMID:
18395224
Author(s):
Esposito, G., Ricagno, S., Corazza, A., Rennella, E., Gumral, D., Mimmi, M.C., Betto, E., Pucillo, C.E.M., Fogolari, F., Viglino, P., Raimondi, S., Giorgetti, S., Bolognesi, B., Merlini, G., Stoppini, M., Bolognesi, M., Bellotti, V.
Reference:
J Mol Biol. 2008 May 9;378(4):887-97.
Download
Entry:
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Structure:
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FASTA
Contact Network:
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JSON
Protein Information
Protein Name:
Beta-2-microglobulin
Alternative Name:
Gene Name:
B2M, CDABP0092, HDCMA22P
Sequence Length:
100
Species:
Homo sapiens
Mutation(s):
W60G
E.C. Number:
UniProt ID:
P61769
Keyword(s):
BETA-2-MICROGLOBULIN
Structure Information
PDB ID:
2VB5
Amyloid Category:
Non-amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
IMMUNE SYSTEM
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Entry:S-0176
PDB ID: 2XKS
CSV
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Close ×
Structure
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Sequence & Sec. Str.
Chain 1
1
I
Q
R
T
P
K
I
Q
V
Y
S
R
H
P
A
E
N
G
K
S
N
F
L
N
C
25
26
Y
V
S
G
F
H
P
S
D
I
E
V
D
L
L
K
N
G
E
R
I
E
K
V
E
50
51
H
S
D
L
S
F
S
K
D
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
K
75
76
D
E
Y
A
C
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
99
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Prion-like conversion during amyloid formation at atomic resolution
They use ?N6, a truncation variant of the naturally amyloidogenic protein Beta(2)-microglobulin (Beta(2)m), to determine the solution structure of a nonnative amyloidogenic intermediate at high resolution. The structure of ?N6 reveals a major repacking of the hydrophobic core to accommodate the nonnative peptidyl-prolyl trans-isomer at Pro32. These structural changes, together with a concomitant pH-dependent enhancement in backbone dynamics on a microsecond-millisecond timescale, give rise to a rare conformer with increased amyloidogenic potential.
Literature
PMID:
21255727
Author(s):
Eichner, T., Kalverda, A.P., Thompson, G.S., Homans, S.W., Radford, S.E.
Reference:
Mol Cell. 2011 Jan 21;41(2):161-72.
Download
Entry:
CSV
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Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Beta-2-microglobulin
Alternative Name:
Gene Name:
B2M, CDABP0092, HDCMA22P
Sequence Length:
99
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P61769
Keyword(s):
BETA-2-MICROGLOBULIN
Structure Information
PDB ID:
2XKS
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
IMMUNE SYSTEM
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Entry:S-0177
PDB ID: 2XKU
CSV
JSON
Close ×
Structure
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Sequence & Sec. Str.
Chain 1
1
M
I
Q
V
Y
S
R
H
P
A
E
N
G
K
S
N
F
L
N
C
Y
V
S
G
F
25
26
H
P
S
D
I
E
V
D
L
L
K
N
G
E
R
I
E
K
V
E
H
S
D
L
S
50
51
F
S
K
D
W
S
F
Y
L
L
Y
Y
T
E
F
T
P
T
E
K
D
E
Y
A
C
75
76
R
V
N
H
V
T
L
S
Q
P
K
I
V
K
W
D
R
D
M
94
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Prion-like conversion during amyloid formation at atomic resolution
Prion-like conversion during amyloid formation at atomic resolution. They use ?N6, a truncation variant of the naturally amyloidogenic protein Beta(2)-microglobulin (Beta(2)m), to determine the solution structure of a nonnative amyloidogenic intermediate at high resolution. The structure of ?N6 reveals a major repacking of the hydrophobic core to accommodate the nonnative peptidyl-prolyl trans-isomer at Pro32. These structural changes, together with a concomitant pH-dependent enhancement in backbone dynamics on a microsecond-millisecond timescale, give rise to a rare conformer with increased amyloidogenic potential.
Literature
PMID:
21255727
Author(s):
Eichner, T., Kalverda, A.P., Thompson, G.S., Homans, S.W., Radford, S.E.
Reference:
Mol Cell. 2011 Jan 21;41(2):161-72.
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:
94
Species:
Homo sapiens
Mutation(s):
[del]N-terminal (6)
E.C. Number:
UniProt ID:
P61769
Keyword(s):
BETA-2-MICROGLOBULIN
Structure Information
PDB ID:
2XKU
Amyloid Category:
Amyloid
Type:
Protein
Global Stoichiometry:
Monomer - A
PDB Classification:
IMMUNE SYSTEM
Method:
SOLUTION NMR
Resolution (
Å
):
R free:
Entry:S-0178
PDB ID: 2Y29
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
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 segment KLVFFA from the amyloid-beta peptide (Ab, residues 16-21), alternate polymorph III
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., 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:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
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:
2Y29
Amyloid Category:
Amyloid
Type:
Peptide
Global Stoichiometry:
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.3
R free:
0.26
Entry:S-0179
PDB ID: 2Y2A
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
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 segment KLVFFA from the amyloid-beta peptide (Ab, residues 16-21), alternate polymorph I
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., 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.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
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:
2Y2A
Amyloid Category:
Amyloid
Type:
Peptide
Global Stoichiometry:
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.91
R free:
0.248
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
Entry:S-0180
PDB ID: 2Y3J
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Structure
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Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
A
I
I
G
L
M
6
Chain 2
1
A
I
I
G
L
M
6
Chain 3
1
A
I
I
G
L
M
6
Chain 4
1
A
I
I
G
L
M
6
Chain 5
1
A
I
I
G
L
M
6
Chain 6
1
A
I
I
G
L
M
6
Chain 7
1
A
I
I
G
L
M
6
Chain 8
1
A
I
I
G
L
M
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Structure of segment AIIGLM from the amyloid-beta peptide (Ab, residues 30-35)
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., 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.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
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:
2Y3J
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 8-mer - A8
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.99
R free:
0.267
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