SMTL ID : 8fcg.1

Cryo-EM structure of Chikungunya virus asymmetric unit

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

5 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PCW.1: 14 residues within 4Å: Chain A: T.396, L.397, G.398, V.399, I.402 Chain E: P.348, I.352, Y.355, Y.359, M.362, T.363, V.366, V.369 Ligands: PCW.2 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:P.348, E:I.352, E:Y.355, E:Y.359, E:Y.359, E:V.366, E:V.369, A:I.402 Hydrogen bonds: A:T.396 PCW.2: 9 residues within 4Å: Chain A: Q.400, V.410, Q.411, I.413, T.414, L.419 Chain E: V.366, A.370 Ligands: PCW.1 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:I.413, A:T.414, A:L.419, E:V.366, E:A.370 Hydrogen bonds: A:Q.411 PCW.3: 12 residues within 4Å: Chain B: L.397, G.398, V.399, W.409, V.410, I.413 Chain F: P.348, I.352, Y.355, Y.359, M.362, F.372 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain F Hydrophobic interactions: B:L.397, B:W.409, B:V.410, B:I.413, F:P.348, F:Y.355, F:Y.359, F:Y.359, F:F.372 PCW.4: 13 residues within 4Å: Chain C: G.398, V.399, Q.400, D.401, S.403, W.409 Chain G: P.348, I.351, I.352, Y.355, Y.359, M.362, V.366 6 PLIP interactions: 5 interactions with chain G, 1 interactions with chain C Hydrophobic interactions: G:P.348, G:I.351, G:I.352, G:Y.359, G:V.366, C:W.409 PCW.5: 9 residues within 4Å: Chain D: L.397, V.399 Chain H: P.348, I.351, I.352, Y.355, Y.359, M.362, V.366 8 PLIP interactions: 6 interactions with chain H, 2 interactions with chain D Hydrophobic interactions: H:P.348, H:I.351, H:Y.355, H:Y.355, H:Y.359, H:V.366, D:V.399, D:V.399

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chmielewski, D. et al., Cryogenic electron microscopy and tomography reveal imperfect icosahedral symmetry in alphaviruses. Pnas Nexus (2024)

Release Date

2024-03-20

Peptides

E1 glycoprotein: ABCD
E2 glycoprotein: EFGH
Capsid protein: IJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Membrane

We predict this structure to be a membrane protein.
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E1 glycoprotein

E2 glycoprotein

Capsid protein

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