Home
Links
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)
Tutorial
Statistics
Download
Contact Us
Home
Tutorial
Statistics
Download
Contact Us
Links
APR Prediction Models:
GAP (Generalized Aggregation Proneness)
ANuPP (Prediciton of Nucleating APRs)
V
L
AmY-Pred (Predicting antibody light chain aggregation)
Aggregation Kinetics Prediction Models:
AggreRATE-Disc (Classifying Aggregating Point Mutation)
AggreRATE-Pred (Predicting Aggregation Rate for Point Mutation)
AbsoluRATE (Predicting Absolute aggregation rate)
Amylo-Pipe (Comprehensive aggregation prediction)
Structure database of aggregation related proteins and peptides
Select a Field to filter:
help
Protein Name
Peptide Sequence
Entry ID
PDB ID
Method
Enter the query text:
help
Select a structure type:
help
All
Protein/Peptide
Fibril
Aggregating complex
Inhibitor complex
Fibril complex
Protein complex
Submit
Reset
Max. of 30 records would be displayed in a single page.
Patterns can be used in the search.
«
1
2
12
13
14
15
16
17
(current)
18
19
»
Displaying 481 to 510 records out of 565 records fetched.
Entry
PDB ID
Protein
Name
Species
Length
Mutation(s)
Class
Type
Method
Resolution (
Å
)
PMID
S-0481
5W4I
Amyloid-beta
Homo sapiens
16
No
Amyloid
Peptide
X-RAY DIFFRACTION
2.03
29028351
S-0482
5W4J
Amyloid-beta
Homo sapiens
16
No
Amyloid
Peptide
X-RAY DIFFRACTION
2.08
29028351
S-0483
5W50
TAR DNA-binding protein 43
Homo sapiens
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.4
29531287
S-0484
5W52
TAR DNA-binding protein 43
Homo sapiens
11
No
Amyloid
Fibril
ELECTRON CRYSTALLOGRAPHY
1.4
29531287
S-0485
5W7V
TAR DNA-binding protein 43
Homo sapiens
11
No
Amyloid
Fibril
ELECTRON MICROSCOPY
3.8
29531287
S-0486
5WHN
TAR DNA-binding protein 43
Homo sapiens
6
No
Non-amyloid
Fibril
X-RAY DIFFRACTION
1.1
29786080
S-0487
5WHP
TAR DNA-binding protein 43
Homo sapiens
6
A315T
Amyloid
Fibril
X-RAY DIFFRACTION
1.0
29786080
S-0488
5WIA
TAR DNA-binding protein 43
Homo sapiens
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.0
29786080
S-0489
5WIQ
TAR DNA-binding protein 43
Homo sapiens
7
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.25
29786080
S-0490
5WKB
TAR DNA-binding protein 43
Homo sapiens
6
A315E
Non-amyloid
Fibril
ELECTRON CRYSTALLOGRAPHY
1.0
29786080
S-0491
5WKD
TAR DNA-binding protein 43
Homo sapiens
7
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.8
29786080
S-0492
5WMJ
Superoxide dismutase [Cu-Zn]
Homo sapiens
6
No
Non-amyloid
Fibril
X-RAY DIFFRACTION
1.4
29453800
S-0493
5WOR
Superoxide dismutase [Cu-Zn]
Homo sapiens
11
G37R
Non-amyloid
Fibril
X-RAY DIFFRACTION
2.77
29453800
S-0494
5XRR
RNA-binding protein FUS
Homo sapiens
6
No
Non-amyloid
Peptide
X-RAY DIFFRACTION
1.5
29610493
S-0495
5XSG
RNA-binding protein FUS
Homo sapiens
6
No
Non-amyloid
Peptide
ELECTRON CRYSTALLOGRAPHY
0.73
29610493
S-0496
5ZCK
Receptor-interacting serine/threonine-protein kinase 3
Homo sapiens
4
No
Amyloid
Peptide
X-RAY DIFFRACTION
1.27
29681455
S-0497
5ZGD
hnRNPA1
Homo sapiens
9
No
Amyloid
Peptide
X-RAY DIFFRACTION
1.4
S-0498
5ZGL
Heterogeneous nuclear ribonucleoprotein A1
Homo sapiens
7
No
Non-amyloid
Peptide
X-RAY DIFFRACTION
0.95
S-0499
5ZMZ
Receptor-interacting serine/threonine-protein kinase 1
Homo sapiens
4
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.4
S-0500
6A6B
Alpha-synuclein
Homo sapiens
63
No
Amyloid
Fibril
ELECTRON MICROSCOPY
3.07
30065316
S-0501
6AXZ
Major prion protein
Myodes glareolus
9
No
Amyloid
Fibril
ELECTRON CRYSTALLOGRAPHY
0.75
29335561
S-0502
6B79
Superoxide dismutase [Cu-Zn]
Homo sapiens
11
G37R
Non-amyloid
Fibril
X-RAY DIFFRACTION
1.8
29453800
S-0503
6BTK
Major prion protein
Myodes glareolus
9
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.1
29335561
S-0504
6BWZ
RNA-binding protein FUS
Homo sapiens
6
No
Non-amyloid
Fibril
X-RAY DIFFRACTION
1.1
29439243
S-0505
6BXV
RNA-binding protein FUS
Homo sapiens
8
No
Non-amyloid
Fibril
X-RAY DIFFRACTION
1.1
29439243
S-0506
6BXX
Heterogeneous nuclear ribonucleoprotein A1
Homo sapiens
6
No
Non-amyloid
Fibril
X-RAY DIFFRACTION
1.1
29439243
S-0507
6BZM
Nuclear pore complex protein Nup98-Nup96
Homo sapiens
8
No
Non-amyloid
Fibril
ELECTRON CRYSTALLOGRAPHY
0.9
29439243
S-0508
6BZP
RNA-binding protein FUS
Homo sapiens
6
No
Non-amyloid
Fibril
ELECTRON CRYSTALLOGRAPHY
1.1
29439243
S-0509
6C3F
Transthyretin
Homo sapiens
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.5
29626847
S-0510
6C3G
Transthyretin
Homo sapiens
6
No
Amyloid
Fibril
X-RAY DIFFRACTION
1.6
29626847
Entry:S-0481
PDB ID: 5W4I
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
A
K
L
V
F
F
A
E
A
A
I
I
G
L
M
V
16
Chain 2
1
A
K
L
V
F
F
A
E
A
A
I
I
G
L
M
V
16
Chain 3
1
A
K
L
V
F
F
A
E
A
A
I
I
G
L
M
V
16
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
X-ray crystallographic structure of a beta-hairpin peptide mimic derived from Abeta 16-36. Rigaku data set. (ORN)KLV(MEA)FAE(ORN)AIIGLMV
[ABeta oligomer] The peptide assembles to form a hexamer in the crystal state and that the hexamer is composed of dimers and trimers. Lactate dehydrogenase release assays show that the oligomers formed by the ABeta 16-36 Beta-hairpin peptide are toxic toward neuronally derived SH-SY5Y cells.
Literature
PMID:
29028351
Author(s):
Kreutzer, A.G., Spencer, R.K., McKnelly, K.J., Yoo, S., Hamza, I.L., Salveson, P.J., Nowick, J.S.
Reference:
Biochemistry. 2017 Nov 14;56(45):6061-6071.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Amyloid-beta
Alternative Name:
Gene Name:
Sequence Length:
16
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
A-beta 17_36: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
Structure Information
PDB ID:
5W4I
Amyloid Category:
Amyloid
Type:
Peptide
Global Stoichiometry:
Homo 24-mer - A24
PDB Classification:
DE NOVO PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.03
R free:
0.247
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
CL
A
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
IOD
A
I -1
126.9
IODIDE ION
[I-]
XMBWDFGMSWQBCA-UHFFFAOYSA-M
MEA
A
C10 H13 N O2
179.22
N-METHYLPHENYLALANINE
CN[C@@H](Cc1ccccc1)C(=O)O
SCIFESDRCALIIM-VIFPVBQESA-N
ORN
A
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
CL
B
Cl -1
35.45
CHLORIDE ION
[Cl-]
VEXZGXHMUGYJMC-UHFFFAOYSA-M
IOD
B
I -1
126.9
IODIDE ION
[I-]
XMBWDFGMSWQBCA-UHFFFAOYSA-M
MEA
B
C10 H13 N O2
179.22
N-METHYLPHENYLALANINE
CN[C@@H](Cc1ccccc1)C(=O)O
SCIFESDRCALIIM-VIFPVBQESA-N
ORN
B
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
MEA
C
C10 H13 N O2
179.22
N-METHYLPHENYLALANINE
CN[C@@H](Cc1ccccc1)C(=O)O
SCIFESDRCALIIM-VIFPVBQESA-N
ORN
C
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
Entry:S-0482
PDB ID: 5W4J
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
A
K
V
F
F
A
A
D
A
A
I
I
G
L
M
V
16
Chain 2
1
A
K
V
F
F
A
A
D
A
A
I
I
G
L
M
V
16
Chain 3
1
A
K
V
F
F
A
A
D
A
A
I
I
G
L
M
V
16
Chain 4
1
A
K
V
F
F
A
A
D
A
A
I
I
G
L
M
V
16
Chain 5
1
A
K
V
F
F
A
A
D
A
A
I
I
G
L
M
V
16
Chain 6
1
A
K
V
F
F
A
A
D
A
A
I
I
G
L
M
V
16
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
X-ray crystallographic structure of a beta-hairpin peptide mimic. (ORN)KLV(MEA)FAE(ORN)AIIGLMV
[ABeta oligomer] The peptide assembles to form a hexamer in the crystal state and that the hexamer is composed of dimers and trimers. Lactate dehydrogenase release assays show that the oligomers formed by the ABeta 16-36 Beta-hairpin peptide are toxic toward neuronally derived SH-SY5Y cells.
Literature
PMID:
29028351
Author(s):
Kreutzer, A.G., Spencer, R.K., McKnelly, K.J., Yoo, S., Hamza, I.L., Salveson, P.J., Nowick, J.S.
Reference:
Biochemistry. 2017 Nov 14;56(45):6061-6071.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Amyloid-beta
Alternative Name:
Gene Name:
Sequence Length:
16
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
A-beta 17_36 peptide: ORN-LYS-VAL-PHE-MEA-ALA-ALA-ASP-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
Structure Information
PDB ID:
5W4J
Amyloid Category:
Amyloid
Type:
Peptide
Global Stoichiometry:
Homo 4-mer - A4
PDB Classification:
DE NOVO PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.08
R free:
0.243
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
MEA
A
C10 H13 N O2
179.22
N-METHYLPHENYLALANINE
CN[C@@H](Cc1ccccc1)C(=O)O
SCIFESDRCALIIM-VIFPVBQESA-N
ORN
A
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
MEA
B
C10 H13 N O2
179.22
N-METHYLPHENYLALANINE
CN[C@@H](Cc1ccccc1)C(=O)O
SCIFESDRCALIIM-VIFPVBQESA-N
ORN
B
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
MEA
C
C10 H13 N O2
179.22
N-METHYLPHENYLALANINE
CN[C@@H](Cc1ccccc1)C(=O)O
SCIFESDRCALIIM-VIFPVBQESA-N
ORN
C
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
MEA
D
C10 H13 N O2
179.22
N-METHYLPHENYLALANINE
CN[C@@H](Cc1ccccc1)C(=O)O
SCIFESDRCALIIM-VIFPVBQESA-N
ORN
D
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
MEA
E
C10 H13 N O2
179.22
N-METHYLPHENYLALANINE
CN[C@@H](Cc1ccccc1)C(=O)O
SCIFESDRCALIIM-VIFPVBQESA-N
ORN
E
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
MEA
F
C10 H13 N O2
179.22
N-METHYLPHENYLALANINE
CN[C@@H](Cc1ccccc1)C(=O)O
SCIFESDRCALIIM-VIFPVBQESA-N
ORN
F
C5 H12 N2 O2
132.16
L-ornithine
C(C[C@@H](C(=O)O)N)CN
AHLPHDHHMVZTML-BYPYZUCNSA-N
Entry:S-0483
PDB ID: 5W50
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
L
I
I
K
G
I
6
Chain 2
1
L
I
I
K
G
I
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of the segment, LIIKGI, from the RRM2 of TDP-43, residues 248-253
They show that the 247 DLIIKGISVHI 257 segment from the second RNA-recognition motif (RRM2) forms an array of amyloid polymorphs. These associations include seven distinct interfaces displaying five different symmetry classes of steric zippers. This segment can adopt three different backbone conformations that contribute to its polymorphic capabilities. The polymorphic nature of this segment illustrates at the molecular level how amyloid proteins can form diverse fibril structures.
Literature
PMID:
29531287
Author(s):
Guenther, E.L., Ge, P., Trinh, H., Sawaya, M.R., Cascio, D., Boyer, D.R., Gonen, T., Zhou, Z.H., Eisenberg, D.S.
Reference:
Nat Struct Mol Biol. 2018 Apr;25(4):311-319.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
TAR DNA-binding protein 43
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Q13148
Keyword(s):
TAR DNA-binding protein 43
Structure Information
PDB ID:
5W50
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 12-mer - A12
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.4
R free:
0.207
Entry:S-0484
PDB ID: 5W52
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Sequence & Sec. Str.
Chain 1
1
D
L
I
I
K
G
I
S
V
H
I
11
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
MicroED structure of the segment, DLIIKGISVHI, from the RRM2 of TDP-43, residues 247-257
They show that the 247 DLIIKGISVHI 257 segment from the second RNA-recognition motif (RRM2) forms an array of amyloid polymorphs. These associations include seven distinct interfaces displaying five different symmetry classes of steric zippers. This segment can adopt three different backbone conformations that contribute to its polymorphic capabilities. The polymorphic nature of this segment illustrates at the molecular level how amyloid proteins can form diverse fibril structures.
Literature
PMID:
29531287
Author(s):
Guenther, E.L., Ge, P., Trinh, H., Sawaya, M.R., Cascio, D., Boyer, D.R., Gonen, T., Zhou, Z.H., Eisenberg, D.S.
Reference:
Nat Struct Mol Biol. 2018 Apr;25(4):311-319.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
TAR DNA-binding protein 43
Alternative Name:
Gene Name:
Sequence Length:
11
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Q13148
Keyword(s):
TAR DNA-binding protein 43
Structure Information
PDB ID:
5W52
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 10-mer - A10
PDB Classification:
PROTEIN FIBRIL
Method:
ELECTRON CRYSTALLOGRAPHY
Resolution (
Å
):
1.4
R free:
0.306
Entry:S-0485
PDB ID: 5W7V
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Sequence & Sec. Str.
Chain 1
1
D
L
I
I
K
G
I
S
V
H
I
11
Chain 2
1
D
L
I
I
K
G
I
S
V
H
I
11
Chain 3
1
D
L
I
I
K
G
I
S
V
H
I
11
Chain 4
1
D
L
I
I
K
G
I
S
V
H
I
11
Chain 5
1
D
L
I
I
K
G
I
S
V
H
I
11
Chain 6
1
D
L
I
I
K
G
I
S
V
H
I
11
Chain 7
1
D
L
I
I
K
G
I
S
V
H
I
11
Chain 8
1
D
L
I
I
K
G
I
S
V
H
I
11
Chain 9
1
D
L
I
I
K
G
I
S
V
H
I
11
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
CryoEM structure of the segment, DLIIKGISVHI, assembled into a triple-helical fibril
They show that the 247 DLIIKGISVHI 257 segment from the second RNA-recognition motif (RRM2) forms an array of amyloid polymorphs. These associations include seven distinct interfaces displaying five different symmetry classes of steric zippers. This segment can adopt three different backbone conformations that contribute to its polymorphic capabilities. The polymorphic nature of this segment illustrates at the molecular level how amyloid proteins can form diverse fibril structures.
Literature
PMID:
29531287
Author(s):
Guenther, E.L., Ge, P., Trinh, H., Sawaya, M.R., Cascio, D., Boyer, D.R., Gonen, T., Zhou, Z.H., Eisenberg, D.S.
Reference:
Nat Struct Mol Biol. 2018 Apr;25(4):311-319.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
TAR DNA-binding protein 43
Alternative Name:
Gene Name:
Sequence Length:
11
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Q13148
Keyword(s):
TAR DNA-binding protein 43
Structure Information
PDB ID:
5W7V
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
PDB Classification:
PROTEIN FIBRIL
Method:
ELECTRON MICROSCOPY
Resolution (
Å
):
3.8
R free:
Entry:S-0486
PDB ID: 5WHN
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
N
F
G
A
F
S
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of the segment, NFGAFS, from the low complexity domain of TDP-43, residues 312-317
To uncover the structural origins of two modes of Beta-sheet-rich aggregation (reversible stress granules and irreversible pathogenic amyloid), they have determined ten structures of segments of the LCD of human TDP-43. Six of these segments form steric zippers characteristic of the spines of pathogenic amyloid fibrils; four others form LARKS, the labile amyloid-like interactions characteristic of protein hydrogels and proteins found in membraneless organelles, including stress granules. 312NFGAFS317 forms a LARKS structure and its microcrystalline aggregates are labile
Literature
PMID:
29786080
Author(s):
Guenther, E.L., Cao, Q., Trinh, H., Lu, J., Sawaya, M.R., Cascio, D., Boyer, D.R., Rodriguez, J.A., Hughes, M.P., Eisenberg, D.S.
Reference:
Nat Struct Mol Biol. 2018 Jun;25(6):463-471.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
TAR DNA-binding protein 43
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Q13148
Keyword(s):
Segment of TAR DNA-binding protein 43
Structure Information
PDB ID:
5WHN
Amyloid Category:
Non-amyloid
Type:
Fibril
Global Stoichiometry:
Homo 15-mer - A15
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.1
R free:
0.16
Entry:S-0487
PDB ID: 5WHP
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
N
F
G
T
F
S
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of the segment, NFGTFS, from the A315T familial variant of the low complexity domain of TDP-43, residues 312-317
To uncover the structural origins of two modes of Beta-sheet-rich aggregation (reversible stress granules and irreversible pathogenic amyloid), they have determined ten structures of segments of the LCD of human TDP-43. Six of these segments form steric zippers characteristic of the spines of pathogenic amyloid fibrils; four others form LARKS, the labile amyloid-like interactions characteristic of protein hydrogels and proteins found in membraneless organelles, including stress granules. 312NFGTFS317 aggregates were irreversible.
Literature
PMID:
29786080
Author(s):
Guenther, E.L., Cao, Q., Trinh, H., Lu, J., Sawaya, M.R., Cascio, D., Boyer, D.R., Rodriguez, J.A., Hughes, M.P., Eisenberg, D.S.
Reference:
Nat Struct Mol Biol. 2018 Jun;25(6):463-471.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
TAR DNA-binding protein 43
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
A315T
E.C. Number:
UniProt ID:
Q13148
Keyword(s):
Segment of TAR DNA-binding protein 43
Structure Information
PDB ID:
5WHP
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 10-mer - A10
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.0
R free:
0.09300000
Entry:S-0488
PDB ID: 5WIA
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
N
N
S
Y
S
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of the segment, GNNSYS, from the low complexity domain of TDP-43, residues 370-375
To uncover the structural origins of two modes of Beta-sheet-rich aggregation (reversible stress granules and irreversible pathogenic amyloid), they have determined ten structures of segments of the LCD of human TDP-43. Six of these segments form steric zippers characteristic of the spines of pathogenic amyloid fibrils; four others form LARKS, the labile amyloid-like interactions characteristic of protein hydrogels and proteins found in membraneless organelles, including stress granules. Segments 300GNNQGSN306, 328AALQSS333 and 370GNNSYS375 all form Class 1 steric zippers in which the Beta-sheets are mated face-to-face with the same edges of the sheet oriented up the fibril.
Literature
PMID:
29786080
Author(s):
Guenther, E.L., Cao, Q., Trinh, H., Lu, J., Sawaya, M.R., Cascio, D., Boyer, D.R., Rodriguez, J.A., Hughes, M.P., Eisenberg, D.S.
Reference:
Nat Struct Mol Biol. 2018 Jun;25(6):463-471.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
TAR DNA-binding protein 43
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Q13148
Keyword(s):
TAR DNA-binding protein 43
Structure Information
PDB ID:
5WIA
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 10-mer - A10
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.0
R free:
0.18100000
Entry:S-0489
PDB ID: 5WIQ
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
F
N
G
G
F
G
7
Chain 2
1
G
F
N
G
G
F
G
7
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of the segment, GFNGGFG, from the low complexity domain of TDP-43, residues 396-402
To uncover the structural origins of two modes of Beta-sheet-rich aggregation (reversible stress granules and irreversible pathogenic amyloid), they have determined ten structures of segments of the LCD of human TDP-43. Six of these segments form steric zippers characteristic of the spines of pathogenic amyloid fibrils; four others form LARKS, the labile amyloid-like interactions characteristic of protein hydrogels and proteins found in membraneless organelles, including stress granules. Segment 396GFNGGFG402 forms a Class 4 steric zipper with face-to-back Beta-sheets and up-down orientation.
Literature
PMID:
29786080
Author(s):
Guenther, E.L., Cao, Q., Trinh, H., Lu, J., Sawaya, M.R., Cascio, D., Boyer, D.R., Rodriguez, J.A., Hughes, M.P., Eisenberg, D.S.
Reference:
Nat Struct Mol Biol. 2018 Jun;25(6):463-471.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
TAR DNA-binding protein 43
Alternative Name:
Gene Name:
Sequence Length:
7
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Q13148
Keyword(s):
TAR DNA-binding protein 43
Structure Information
PDB ID:
5WIQ
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 10-mer - A10
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.25
R free:
0.168
Entry:S-0490
PDB ID: 5WKB
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Sequence & Sec. Str.
Chain 1
1
N
F
G
E
F
S
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
MicroED structure of the segment, NFGEFS, from the A315E familial variant of the low complexity domain of TDP-43, residues 312-317
To uncover the structural origins of two modes of Beta-sheet-rich aggregation (reversible stress granules and irreversible pathogenic amyloid), they have determined ten structures of segments of the LCD of human TDP-43. Six of these segments form steric zippers characteristic of the spines of pathogenic amyloid fibrils; four others form LARKS, the labile amyloid-like interactions characteristic of protein hydrogels and proteins found in membraneless organelles, including stress granules. 312NFGEFS317 aggregates were irreversible.
Literature
PMID:
29786080
Author(s):
Guenther, E.L., Cao, Q., Trinh, H., Lu, J., Sawaya, M.R., Cascio, D., Boyer, D.R., Rodriguez, J.A., Hughes, M.P., Eisenberg, D.S.
Reference:
Nat Struct Mol Biol. 2018 Jun;25(6):463-471.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
TAR DNA-binding protein 43
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
A315E
E.C. Number:
UniProt ID:
Q13148
Keyword(s):
TAR DNA-binding protein 43
Structure Information
PDB ID:
5WKB
Amyloid Category:
Non-amyloid
Type:
Fibril
Global Stoichiometry:
Homo 10-mer - A10
PDB Classification:
PROTEIN FIBRIL
Method:
ELECTRON CRYSTALLOGRAPHY
Resolution (
Å
):
1.0
R free:
0.27
Entry:S-0491
PDB ID: 5WKD
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
N
N
Q
G
S
N
7
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of the segment, GNNQGSN, from the low complexity domain of TDP-43, residues 300-306
To uncover the structural origins of two modes of Beta-sheet-rich aggregation (reversible stress granules and irreversible pathogenic amyloid), they have determined ten structures of segments of the LCD of human TDP-43. Six of these segments form steric zippers characteristic of the spines of pathogenic amyloid fibrils; four others form LARKS, the labile amyloid-like interactions characteristic of protein hydrogels and proteins found in membraneless organelles, including stress granules. Segments 300GNNQGSN306, 328AALQSS333 and 370GNNSYS375 all form Class 1 steric zippers in which the Beta-sheets are mated face-to-face with the same edges of the sheet oriented up the fibril.
Literature
PMID:
29786080
Author(s):
Guenther, E.L., Cao, Q., Trinh, H., Lu, J., Sawaya, M.R., Cascio, D., Boyer, D.R., Rodriguez, J.A., Hughes, M.P., Eisenberg, D.S.
Reference:
Nat Struct Mol Biol. 2018 Jun;25(6):463-471.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
TAR DNA-binding protein 43
Alternative Name:
Gene Name:
Sequence Length:
7
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Q13148
Keyword(s):
TAR DNA-binding protein 43
Structure Information
PDB ID:
5WKD
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 10-mer - A10
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.8
R free:
0.195
Entry:S-0492
PDB ID: 5WMJ
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
K
V
W
G
S
I
6
Chain 2
1
K
V
W
G
S
I
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
KVWGSI segment from Superoxide Dismutase 1,residues 30-35
Crystal structures of variants of the cytotoxic oligomer-forming segment residues 28-38 of the ALS-linked protein, SOD1. The crystal structures reveal three different architectures: corkscrew oligomeric structure, nontwisting curved sheet structure and a steric zipper proto-filament structure.
Literature
PMID:
29453800
Author(s):
Sangwan, S., Sawaya, M.R., Murray, K.A., Hughes, M.P., Eisenberg, D.S.
Reference:
Protein Sci. 2018 Jul;27(7):1231-1242.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Superoxide dismutase [Cu-Zn]
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
1.15.1.1
UniProt ID:
P00441
Keyword(s):
Superoxide dismutase [Cu-Zn]
Structure Information
PDB ID:
5WMJ
Amyloid Category:
Non-amyloid
Type:
Fibril
Global Stoichiometry:
Homo 8-mer - A8
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.4
R free:
0.17
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
TFA
B
C2 H F3 O2
114.02
trifluoroacetic acid
C(=O)(C(F)(F)F)O
DTQVDTLACAAQTR-UHFFFAOYSA-N
Entry:S-0493
PDB ID: 5WOR
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
K
V
K
V
W
G
S
I
K
R
L
11
Chain 2
1
K
V
K
V
W
G
S
I
K
R
L
11
Chain 3
1
K
V
K
V
W
G
S
I
K
R
L
11
Chain 4
1
K
V
K
V
W
G
S
I
K
R
L
11
Chain 5
1
K
V
K
V
W
G
S
I
K
R
L
11
Chain 6
1
K
V
K
V
W
G
S
I
K
R
L
11
Chain 7
1
K
V
K
V
W
G
S
I
K
R
L
11
Chain 8
1
K
V
K
V
W
G
S
I
K
R
L
11
Chain 9
1
K
V
K
V
W
G
S
I
K
R
L
11
Chain 10
1
K
V
K
V
W
G
S
I
K
R
L
11
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Corkscrew assembly of SOD1 residues 28-38 with familial mutation G37R
Crystal structures of variants of the cytotoxic oligomer-forming segment residues 28-38 of the ALS-linked protein, SOD1. The crystal structures reveal three different architectures: corkscrew oligomeric structure, nontwisting curved sheet structure and a steric zipper proto-filament structure.
Literature
PMID:
29453800
Author(s):
Sangwan, S., Sawaya, M.R., Murray, K.A., Hughes, M.P., Eisenberg, D.S.
Reference:
Protein Sci. 2018 Jul;27(7):1231-1242.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Superoxide dismutase [Cu-Zn]
Alternative Name:
Gene Name:
Sequence Length:
11
Species:
Homo sapiens
Mutation(s):
G37R
E.C. Number:
1.15.1.1
UniProt ID:
P00441
Keyword(s):
Superoxide dismutase [Cu-Zn]
Structure Information
PDB ID:
5WOR
Amyloid Category:
Non-amyloid
Type:
Fibril
Global Stoichiometry:
Homo 20-mer - A20
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
2.77
R free:
0.247
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
MLI
A
C3 H2 O4 -2
102.05
MALONATE ION
C(C(=O)[O-])C(=O)[O-]
OFOBLEOULBTSOW-UHFFFAOYSA-L
MLI
B
C3 H2 O4 -2
102.05
MALONATE ION
C(C(=O)[O-])C(=O)[O-]
OFOBLEOULBTSOW-UHFFFAOYSA-L
MLI
E
C3 H2 O4 -2
102.05
MALONATE ION
C(C(=O)[O-])C(=O)[O-]
OFOBLEOULBTSOW-UHFFFAOYSA-L
GOL
I
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Entry:S-0494
PDB ID: 5XRR
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
S
Y
S
S
Y
G
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Crystal structure of FUS (54-59) SYSSYG
Two tandem (S/G)Y(S/G) motifs of the human FUS low-complexity domain (FUS LC) form reversible fibrils in a temperature- and phosphorylation-dependent manner. They named these motifs reversible amyloid cores, or RAC1 and RAC2, and determined their atomic structures in fibrillar forms, using microelectron and X-ray diffraction techniques.
Literature
PMID:
29610493
Author(s):
Luo, F., Gui, X., Zhou, H., Gu, J., Li, Y., Liu, X., Zhao, M., Li, D., Li, X., Liu, C.
Reference:
Nat Struct Mol Biol. 2018 Apr;25(4):341-346.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
RNA-binding protein FUS
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P35637
Keyword(s):
RNA-binding protein FUS
Structure Information
PDB ID:
5XRR
Amyloid Category:
Non-amyloid
Type:
Peptide
Global Stoichiometry:
PDB Classification:
RNA BINDING PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.5
R free:
0.24100000
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
ZN
A
Zn 2
65.41
ZINC ION
[Zn+2]
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Entry:S-0495
PDB ID: 5XSG
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Sequence & Sec. Str.
Chain 1
1
S
Y
S
G
Y
S
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Ultrahigh resolution structure of FUS (37-42) SYSGYS determined by MicroED
Two tandem (S/G)Y(S/G) motifs of the human FUS low-complexity domain (FUS LC) form reversible fibrils in a temperature- and phosphorylation-dependent manner. They named these motifs reversible amyloid cores, or RAC1 and RAC2, and determined their atomic structures in fibrillar forms, using microelectron and X-ray diffraction techniques.
Literature
PMID:
29610493
Author(s):
Luo, F., Gui, X., Zhou, H., Gu, J., Li, Y., Liu, X., Zhao, M., Li, D., Li, X., Liu, C.
Reference:
Nat Struct Mol Biol. 2018 Apr;25(4):341-346.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
RNA-binding protein FUS
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P35637
Keyword(s):
RNA-binding protein FUS
Structure Information
PDB ID:
5XSG
Amyloid Category:
Non-amyloid
Type:
Peptide
Global Stoichiometry:
PDB Classification:
RNA BINDING PROTEIN
Method:
ELECTRON CRYSTALLOGRAPHY
Resolution (
Å
):
0.73
R free:
0.289
Entry:S-0496
PDB ID: 5ZCK
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
V
Q
V
G
4
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Structure of the RIP3 core region
The RIPK1-RIPK3 necrosome is an amyloid signaling complex that initiates TNF-induced necroptosis, serving in human immune defense, cancer, and neurodegenerative diseases. RIPK1 and RIPK3 associate through their RIP homotypic interaction motifs with consensus sequences IQIG (RIPK1) and VQVG (RIPK3). They determined the high-resolution structure of the RIPK1-RIPK3 core. RIPK1 and RIPK3 alternately stack to form heterotypic Beta sheets. Two such Beta sheets bind together along a compact hydrophobic interface featuring an unusual ladder of alternating Ser (from RIPK1) and Cys (from RIPK3). The RIPK1-RIPK3 core is the first detailed structure of a hetero-amyloid and provides a potential explanation for the specificity of hetero- over homo-amyloid formation and a structural basis for understanding the mechanisms of signal transduction.
Literature
PMID:
29681455
Author(s):
Mompean, M., Li, W., Li, J., Laage, S., Siemer, A.B., Bozkurt, G., Wu, H., McDermott, A.E.
Reference:
Cell. 2018 May 17;173(5):1244-1253.e10.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Receptor-interacting serine/threonine-protein kinase 3
Alternative Name:
Gene Name:
Sequence Length:
4
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Q9Y572
Keyword(s):
peptide from Receptor-interacting serine/threonine-protein kinase 3
Structure Information
PDB ID:
5ZCK
Amyloid Category:
Amyloid
Type:
Peptide
Global Stoichiometry:
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.27
R free:
0.153
Entry:S-0497
PDB ID: 5ZGD
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
F
G
G
N
D
N
F
G
9
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
hnRNPA1 reversible amyloid core GFGGNDNFG (residues 209-217) determined by X-ray
They synthesized the two segments and observed that both of them formed reversible fibrils and hydrogels, similar to the behavior of hnRAC1. The reversible fibrils formed by hnRAC2 and hnRAC3 exhibited typical cross-? architectures by X-ray fibril diffraction.
Literature
PMID:
Author(s):
Gui, X., Xie, M., Zhao, M., Luo, F., He, J., Li, D., Liu, C.
Reference:
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
hnRNPA1
Alternative Name:
Gene Name:
Sequence Length:
9
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHE-GLY
Structure Information
PDB ID:
5ZGD
Amyloid Category:
Amyloid
Type:
Peptide
Global Stoichiometry:
PDB Classification:
RNA BINDING PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.4
R free:
0.159
Entry:S-0498
PDB ID: 5ZGL
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
G
G
Y
G
G
S
7
Chain 2
1
G
G
G
Y
G
G
S
7
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
hnRNP A1 segment GGGYGGS (residues 234-240); Structural basis for reversible amyloids of hnRNPA1 as functional ensembles behind stress granule and en route to pathological amyloids
This segment does not form fibrils or hydrogels and thus may not be an amyloid core. The structure showed an unfolded conformation with no fibrillar packing and used as a control in the experiment.
Literature
PMID:
Author(s):
Xie, M., Luo, F., Gui, X., Zhao, M., He, J., Li, D., Liu, C.
Reference:
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Heterogeneous nuclear ribonucleoprotein A1
Alternative Name:
Gene Name:
Sequence Length:
7
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P09651
Keyword(s):
7-mer peptide from Heterogeneous nuclear ribonucleoprotein A1
Structure Information
PDB ID:
5ZGL
Amyloid Category:
Non-amyloid
Type:
Peptide
Global Stoichiometry:
PDB Classification:
RNA BINDING PROTEIN
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
0.95
R free:
0.121
Entry:S-0499
PDB ID: 5ZMZ
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
I
Q
I
G
4
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Amyloid core of RIP1
Amyloid core of RIP1
Literature
PMID:
Author(s):
Li, J.X., Zheng, J.
Reference:
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Receptor-interacting serine/threonine-protein kinase 1
Alternative Name:
Gene Name:
Sequence Length:
4
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Q13546
Keyword(s):
Amyloid core of RIP1
Structure Information
PDB ID:
5ZMZ
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
PDB Classification:
PROTEIN BINDING
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.4
R free:
0.275
Entry:S-0500
PDB ID: 6A6B
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Sequence & Sec. Str.
Chain 1
1
V
L
Y
V
G
S
K
T
K
E
G
V
V
H
G
V
A
T
V
A
E
K
T
K
E
25
26
Q
V
T
N
V
G
G
A
V
V
T
G
V
T
A
V
A
Q
K
T
V
E
G
A
G
50
51
S
I
A
A
A
T
G
F
V
K
K
D
Q
63
Chain 2
1
V
L
Y
V
G
S
K
T
K
E
G
V
V
H
G
V
A
T
V
A
E
K
T
K
E
25
26
Q
V
T
N
V
G
G
A
V
V
T
G
V
T
A
V
A
Q
K
T
V
E
G
A
G
50
51
S
I
A
A
A
T
G
F
V
K
K
D
Q
63
Chain 3
1
V
L
Y
V
G
S
K
T
K
E
G
V
V
H
G
V
A
T
V
A
E
K
T
K
E
25
26
Q
V
T
N
V
G
G
A
V
V
T
G
V
T
A
V
A
Q
K
T
V
E
G
A
G
50
51
S
I
A
A
A
T
G
F
V
K
K
D
Q
63
Chain 4
1
V
L
Y
V
G
S
K
T
K
E
G
V
V
H
G
V
A
T
V
A
E
K
T
K
E
25
26
Q
V
T
N
V
G
G
A
V
V
T
G
V
T
A
V
A
Q
K
T
V
E
G
A
G
50
51
S
I
A
A
A
T
G
F
V
K
K
D
Q
63
Chain 5
1
V
L
Y
V
G
S
K
T
K
E
G
V
V
H
G
V
A
T
V
A
E
K
T
K
E
25
26
Q
V
T
N
V
G
G
A
V
V
T
G
V
T
A
V
A
Q
K
T
V
E
G
A
G
50
51
S
I
A
A
A
T
G
F
V
K
K
D
Q
63
Chain 6
1
V
L
Y
V
G
S
K
T
K
E
G
V
V
H
G
V
A
T
V
A
E
K
T
K
E
25
26
Q
V
T
N
V
G
G
A
V
V
T
G
V
T
A
V
A
Q
K
T
V
E
G
A
G
50
51
S
I
A
A
A
T
G
F
V
K
K
D
Q
63
Chain 7
1
V
L
Y
V
G
S
K
T
K
E
G
V
V
H
G
V
A
T
V
A
E
K
T
K
E
25
26
Q
V
T
N
V
G
G
A
V
V
T
G
V
T
A
V
A
Q
K
T
V
E
G
A
G
50
51
S
I
A
A
A
T
G
F
V
K
K
D
Q
63
Chain 8
1
V
L
Y
V
G
S
K
T
K
E
G
V
V
H
G
V
A
T
V
A
E
K
T
K
E
25
26
Q
V
T
N
V
G
G
A
V
V
T
G
V
T
A
V
A
Q
K
T
V
E
G
A
G
50
51
S
I
A
A
A
T
G
F
V
K
K
D
Q
63
Chain 9
1
V
L
Y
V
G
S
K
T
K
E
G
V
V
H
G
V
A
T
V
A
E
K
T
K
E
25
26
Q
V
T
N
V
G
G
A
V
V
T
G
V
T
A
V
A
Q
K
T
V
E
G
A
G
50
51
S
I
A
A
A
T
G
F
V
K
K
D
Q
63
Chain 10
1
V
L
Y
V
G
S
K
T
K
E
G
V
V
H
G
V
A
T
V
A
E
K
T
K
E
25
26
Q
V
T
N
V
G
G
A
V
V
T
G
V
T
A
V
A
Q
K
T
V
E
G
A
G
50
51
S
I
A
A
A
T
G
F
V
K
K
D
Q
63
Chain 11
1
V
L
Y
V
G
S
K
T
K
E
G
V
V
H
G
V
A
T
V
A
E
K
T
K
E
25
26
Q
V
T
N
V
G
G
A
V
V
T
G
V
T
A
V
A
Q
K
T
V
E
G
A
G
50
51
S
I
A
A
A
T
G
F
V
K
K
D
Q
63
Chain 12
1
V
L
Y
V
G
S
K
T
K
E
G
V
V
H
G
V
A
T
V
A
E
K
T
K
E
25
26
Q
V
T
N
V
G
G
A
V
V
T
G
V
T
A
V
A
Q
K
T
V
E
G
A
G
50
51
S
I
A
A
A
T
G
F
V
K
K
D
Q
63
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
cryo-em structure of alpha-synuclein fiber
They determined a fibril structure of full-length Alpha-syn (1-140). They were able to build the fibril structure comprising residues 37-99. The Alpha-syn amyloid fibril structure shows two protofilaments intertwining along an approximate 2 1 screw axis into a left-handed helix. Each protofilament features a Greek key-like topology.
Literature
PMID:
30065316
Author(s):
Li, Y., Zhao, C., Luo, F., Liu, Z., Gui, X., Luo, Z., Zhang, X., Li, D., Liu, C., Li, X.
Reference:
Cell Res. 2018 Sep;28(9):897-903.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Alpha-synuclein
Alternative Name:
Non-A beta component of AD amyloid, Non-A4 component of amyloid precursor
Gene Name:
SNCA, NACP, PARK1
Sequence Length:
63
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P37840
Keyword(s):
Alpha-synuclein
Structure Information
PDB ID:
6A6B
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Monomer - A
PDB Classification:
PROTEIN FIBRIL
Method:
ELECTRON MICROSCOPY
Resolution (
Å
):
3.07
R free:
Entry:S-0501
PDB ID: 6AXZ
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Sequence & Sec. Str.
Chain 1
1
Q
Y
N
N
Q
N
N
F
V
9
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Segment from bank vole prion protein 168-176 QYNNQNNFV
They reveal the structure of a protofibril formed by a wild-type segment from the Beta2-Alpha2 loop of the bank vole prion protein. The structure of this protofibril reveals a stabilizing network of hydrogen bonds that link polar zippers within a sheet, producing motifs we have named 'polar clasps'.
Literature
PMID:
29335561
Author(s):
Gallagher-Jones, M., Glynn, C., Boyer, D.R., Martynowycz, M.W., Hernandez, E., Miao, J., Zee, C.T., Novikova, I.V., Goldschmidt, L., McFarlane, H.T., Helguera, G.F., Evans, J.E., Sawaya, M.R., Cascio, D., Eisenberg, D.S., Gonen, T., Rodriguez, J.A.
Reference:
Nat Struct Mol Biol. 2018 Feb;25(2):131-134.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Major prion protein
Alternative Name:
Gene Name:
Sequence Length:
9
Species:
Myodes glareolus
Mutation(s):
No
E.C. Number:
UniProt ID:
Q8VHV5
Keyword(s):
Major prion protein
Structure Information
PDB ID:
6AXZ
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 10-mer - A10
PDB Classification:
PROTEIN FIBRIL
Method:
ELECTRON CRYSTALLOGRAPHY
Resolution (
Å
):
0.75
R free:
0.24600000
Entry:S-0502
PDB ID: 6B79
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
K
X
K
V
W
G
S
I
K
R
L
11
Chain 2
1
K
X
K
V
W
G
S
I
K
R
L
11
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Curved pair of sheets formed from SOD1 residues 28-38 with familial mutation G37R
Crystal structures of variants of the cytotoxic oligomer-forming segment residues 28-38 of the ALS-linked protein, SOD1. The crystal structures reveal three different architectures: corkscrew oligomeric structure, nontwisting curved sheet structure and a steric zipper proto-filament structure.
Literature
PMID:
29453800
Author(s):
Sangwan, S., Sawaya, M.R., Murray, K.A., Hughes, M.P., Eisenberg, D.S.
Reference:
Protein Sci. 2018 Jul;27(7):1231-1242.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Superoxide dismutase [Cu-Zn]
Alternative Name:
Gene Name:
Sequence Length:
11
Species:
Homo sapiens
Mutation(s):
G37R
E.C. Number:
1.15.1.1
UniProt ID:
P00441
Keyword(s):
Superoxide dismutase [Cu-Zn]
Structure Information
PDB ID:
6B79
Amyloid Category:
Non-amyloid
Type:
Fibril
Global Stoichiometry:
Homo 8-mer - A8
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.8
R free:
0.267
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
A8E
A
C5 H8 Br N O2
194.03
(2S)-2-amino-4-bromopent-4-enoic acid
C=C(C[C@@H](C(=O)O)N)Br
YTCSGBSYHNQHFD-BYPYZUCNSA-N
ORA
A
C16 H12 N2 O7 S2
408.41
7-hydroxy-8-[(E)-phenyldiazenyl]naphthalene-1,3-disulfonic acid
c1ccc(cc1)/N=N/c2c(ccc3c2c(cc(c3)S(=O)(=O)O)S(=O)(=O)O)O
MPVDXIMFBOLMNW-ISLYRVAYSA-N
A8E
B
C5 H8 Br N O2
194.03
(2S)-2-amino-4-bromopent-4-enoic acid
C=C(C[C@@H](C(=O)O)N)Br
YTCSGBSYHNQHFD-BYPYZUCNSA-N
Entry:S-0503
PDB ID: 6BTK
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
Q
Y
N
N
Q
N
N
F
V
9
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
Segment from bank vole prion protein 168-176 QYNNQNNFV
They reveal the structure of a protofibril formed by a wild-type segment from the Beta2-Alpha2 loop of the bank vole prion protein. The structure of this protofibril reveals a stabilizing network of hydrogen bonds that link polar zippers within a sheet, producing motifs we have named 'polar clasps'.
Literature
PMID:
29335561
Author(s):
Gallagher-Jones, M., Glynn, C., Boyer, D.R., Martynowycz, M.W., Hernandez, E., Miao, J., Zee, C.T., Novikova, I.V., Goldschmidt, L., McFarlane, H.T., Helguera, G.F., Evans, J.E., Sawaya, M.R., Cascio, D., Eisenberg, D.S., Gonen, T., Rodriguez, J.A.
Reference:
Nat Struct Mol Biol. 2018 Feb;25(2):131-134.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Major prion protein
Alternative Name:
Gene Name:
Sequence Length:
9
Species:
Myodes glareolus
Mutation(s):
No
E.C. Number:
UniProt ID:
Q8VHV5
Keyword(s):
Major prion protein
Structure Information
PDB ID:
6BTK
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 10-mer - A10
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.1
R free:
0.162
Entry:S-0504
PDB ID: 6BWZ
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
S
Y
S
G
Y
S
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
SYSGYS from low-complexity domain of FUS, residues 37-42; kinked beta sheets
They determined the atomic structures of five segments from protein low-complexity domains associated with membraneless assemblies. Their common structural feature is the stacking of segments into kinked Beta sheets that pair into protofilaments. Unlike steric zippers of amyloid fibrils, the kinked sheets interact weakly through polar atoms and aromatic side chains. SYSGYS from low-complexity domain of FUS, residues 37-42.
Literature
PMID:
29439243
Author(s):
Hughes, M.P., Sawaya, M.R., Boyer, D.R., Goldschmidt, L., Rodriguez, J.A., Cascio, D., Chong, L., Gonen, T., Eisenberg, D.S.
Reference:
Science. 2018 Feb 9;359(6376):698-701.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
RNA-binding protein FUS
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P35637
Keyword(s):
SYSGYS peptide from low-complexity domain of FUS
Structure Information
PDB ID:
6BWZ
Amyloid Category:
Non-amyloid
Type:
Fibril
Global Stoichiometry:
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.1
R free:
0.165
Entry:S-0505
PDB ID: 6BXV
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
S
Y
S
S
Y
G
Q
S
8
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
SYSSYGQS from low-complexity domain of FUS, residues 54-61
They determined the atomic structures of five segments from protein low-complexity domains associated with membraneless assemblies. Their common structural feature is the stacking of segments into kinked Beta sheets that pair into protofilaments. Unlike steric zippers of amyloid fibrils, the kinked sheets interact weakly through polar atoms and aromatic side chains. SYSSYGQS from low-complexity domain of FUS, residues 54-61.
Literature
PMID:
29439243
Author(s):
Hughes, M.P., Sawaya, M.R., Boyer, D.R., Goldschmidt, L., Rodriguez, J.A., Cascio, D., Chong, L., Gonen, T., Eisenberg, D.S.
Reference:
Science. 2018 Feb 9;359(6376):698-701.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
RNA-binding protein FUS
Alternative Name:
Gene Name:
Sequence Length:
8
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P35637
Keyword(s):
FUS
Structure Information
PDB ID:
6BXV
Amyloid Category:
Non-amyloid
Type:
Fibril
Global Stoichiometry:
Homo 10-mer - A10
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.1
R free:
0.14800000
Entry:S-0506
PDB ID: 6BXX
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
G
Y
N
G
F
G
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
GYNGFG from low-complexity domain of hnRNPA1, residues 243-248
They determined the atomic structures of five segments from protein low-complexity domains associated with membraneless assemblies. Their common structural feature is the stacking of segments into kinked Beta sheets that pair into protofilaments. Unlike steric zippers of amyloid fibrils, the kinked sheets interact weakly through polar atoms and aromatic side chains. GYNGFG from low-complexity domain of hnRNPA1, residues 243-248.
Literature
PMID:
29439243
Author(s):
Hughes, M.P., Sawaya, M.R., Boyer, D.R., Goldschmidt, L., Rodriguez, J.A., Cascio, D., Chong, L., Gonen, T., Eisenberg, D.S.
Reference:
Science. 2018 Feb 9;359(6376):698-701.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Heterogeneous nuclear ribonucleoprotein A1
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P09651
Keyword(s):
hnRNPA1
Structure Information
PDB ID:
6BXX
Amyloid Category:
Non-amyloid
Type:
Fibril
Global Stoichiometry:
Homo 10-mer - A10
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.1
R free:
0.086
Entry:S-0507
PDB ID: 6BZM
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Sequence & Sec. Str.
Chain 1
1
G
F
G
N
F
G
T
S
8
Chain 2
1
G
F
G
N
F
G
T
S
8
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
GFGNFGTS from low-complexity/FG repeat domain of Nup98, residues 116-123
They determined the atomic structures of five segments from protein low-complexity domains associated with membraneless assemblies. Their common structural feature is the stacking of segments into kinked Beta sheets that pair into protofilaments. Unlike steric zippers of amyloid fibrils, the kinked sheets interact weakly through polar atoms and aromatic side chains. GFGNFGTS from low-complexity/FG repeat domain of Nup98, residues 116-123.
Literature
PMID:
29439243
Author(s):
Hughes, M.P., Sawaya, M.R., Boyer, D.R., Goldschmidt, L., Rodriguez, J.A., Cascio, D., Chong, L., Gonen, T., Eisenberg, D.S.
Reference:
Science. 2018 Feb 9;359(6376):698-701.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Nuclear pore complex protein Nup98-Nup96
Alternative Name:
Gene Name:
Sequence Length:
8
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P52948
Keyword(s):
Nuclear pore complex protein Nup98-Nup96
Structure Information
PDB ID:
6BZM
Amyloid Category:
Non-amyloid
Type:
Fibril
Global Stoichiometry:
Homo 10-mer - A10
PDB Classification:
PROTEIN FIBRIL
Method:
ELECTRON CRYSTALLOGRAPHY
Resolution (
Å
):
0.9
R free:
0.264
Entry:S-0508
PDB ID: 6BZP
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Sequence & Sec. Str.
Chain 1
1
S
T
G
G
Y
G
6
Chain 2
1
S
T
G
G
Y
G
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
STGGYG from low-complexity domain of FUS, residues 77-82
They determined the atomic structures of five segments from protein low-complexity domains associated with membraneless assemblies. Their common structural feature is the stacking of segments into kinked Beta sheets that pair into protofilaments. Unlike steric zippers of amyloid fibrils, the kinked sheets interact weakly through polar atoms and aromatic side chains. STGGYG from low-complexity domain of FUS, residues 77-82.
Literature
PMID:
29439243
Author(s):
Hughes, M.P., Sawaya, M.R., Boyer, D.R., Goldschmidt, L., Rodriguez, J.A., Cascio, D., Chong, L., Gonen, T., Eisenberg, D.S.
Reference:
Science. 2018 Feb 9;359(6376):698-701.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
RNA-binding protein FUS
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
P35637
Keyword(s):
RNA-binding protein FUS
Structure Information
PDB ID:
6BZP
Amyloid Category:
Non-amyloid
Type:
Fibril
Global Stoichiometry:
Homo 10-mer - A10
PDB Classification:
PROTEIN FIBRIL
Method:
ELECTRON CRYSTALLOGRAPHY
Resolution (
Å
):
1.1
R free:
0.255
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
TOE
B
C7 H16 O4
164.2
2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL
COCCOCCOCCO
JLGLQAWTXXGVEM-UHFFFAOYSA-N
Entry:S-0509
PDB ID: 6C3F
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
I
Y
K
V
E
I
6
Chain 2
1
I
Y
K
V
E
I
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
AMYLOID FORMING PEPTIDE IYKVEI FROM TRANSTHYRETIN
They study amyloidogenic segments of transthyretin (TTR). TTR is a transporter of thyroxine and retinol in the blood and cerebrospinal fluid. When mutated and/or as a result of aging, TTR aggregates into amyloid fibrils that accumulate in organs such as the heart. The segments from the C-terminal region of TTR form in-register steric-zippers with highly-interdigitated, wet interfaces, whereas the Beta-strand B from the N-terminal region of TTR forms an out-of-register assembly, previously associated with oligomeric formation.
Literature
PMID:
29626847
Author(s):
Saelices, L., Sievers, S.A., Sawaya, M.R., Eisenberg, D.S.
Reference:
Protein Sci. 2018 Jul;27(7):1295-1303.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
ILE-TYR-LYS-VAL-GLU-ILE
Structure Information
PDB ID:
6C3F
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 20-mer - A20
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.5
R free:
0.262
Ligand Information
Ligand ID
Chain ID
Ligand Formula
Ligand MW
Ligand Name
Ligand SMILES
InChI Key
TFA
A
C2 H F3 O2
114.02
trifluoroacetic acid
C(=O)(C(F)(F)F)O
DTQVDTLACAAQTR-UHFFFAOYSA-N
Entry:S-0510
PDB ID: 6C3G
CSV
JSON
Close ×
Structure
Press 'p' to pause
View interactive contact network
Protein Contacts Atlas
Sequence & Sec. Str.
Chain 1
1
K
A
L
G
I
S
6
Chain 2
1
K
A
L
G
I
S
6
Helix: Magenta; Strand: Yellow; Coil & Turn: White.
Charged residues and Proline are highlighed in blue.
Description
AMYLOID FORMING PEPTIDE KALGIS FROM TRANSTHYRETIN
They study amyloidogenic segments of transthyretin (TTR). TTR is a transporter of thyroxine and retinol in the blood and cerebrospinal fluid. When mutated and/or as a result of aging, TTR aggregates into amyloid fibrils that accumulate in organs such as the heart. The segments from the C-terminal region of TTR form in-register steric-zippers with highly-interdigitated, wet interfaces, whereas the Beta-strand B from the N-terminal region of TTR forms an out-of-register assembly, previously associated with oligomeric formation.
Literature
PMID:
29626847
Author(s):
Saelices, L., Sievers, S.A., Sawaya, M.R., Eisenberg, D.S.
Reference:
Protein Sci. 2018 Jul;27(7):1295-1303.
Download
Entry:
CSV
JSON
Structure:
PDB
CIF
FASTA
Contact Network:
CSV
JSON
Protein Information
Protein Name:
Transthyretin
Alternative Name:
Gene Name:
Sequence Length:
6
Species:
Homo sapiens
Mutation(s):
No
E.C. Number:
UniProt ID:
Keyword(s):
LYS-ALA-LEU-GLY-ILE-SER
Structure Information
PDB ID:
6C3G
Amyloid Category:
Amyloid
Type:
Fibril
Global Stoichiometry:
Homo 20-mer - A20
PDB Classification:
PROTEIN FIBRIL
Method:
X-RAY DIFFRACTION
Resolution (
Å
):
1.6
R free:
0.212
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
GOL
B
C3 H8 O3
92.09
GLYCEROL
C(C(CO)O)O
PEDCQBHIVMGVHV-UHFFFAOYSA-N
«
1
2
12
13
14
15
16
17
(current)
18
19
»
