SMTL ID : 7bzn.3 (3 other biounits)

Cryo-EM structure of mature Coxsackievirus A10 at pH 7.4

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-6-6-mer

Ligands

6 x SPH: SPHINGOSINE(Non-covalent)

SPH.1: 16 residues within 4Å: Chain A: I.110, D.111, I.112, F.134, F.136, Y.152, Y.154, V.189, V.191, Y.200, W.202, N.227, M.229, F.232, M.252 Chain C: I.24 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:I.110, A:I.110, A:I.112, A:F.134, A:F.134, A:F.136, A:Y.152, A:Y.154, A:Y.154, A:Y.154, A:V.189, A:V.191, A:V.191, A:Y.200, A:M.229, A:F.232, C:I.24, C:I.24 Hydrogen bonds: A:I.110, A:D.111, A:D.111, A:I.112, A:N.227 SPH.2: 16 residues within 4Å: Chain E: I.110, D.111, I.112, F.134, F.136, Y.152, Y.154, V.189, V.191, Y.200, W.202, N.227, M.229, F.232, M.252 Chain G: I.24 23 PLIP interactions: 21 interactions with chain E, 2 interactions with chain G Hydrophobic interactions: E:I.110, E:I.110, E:I.112, E:F.134, E:F.134, E:F.136, E:Y.152, E:Y.154, E:Y.154, E:Y.154, E:V.189, E:V.191, E:V.191, E:Y.200, E:M.229, E:F.232, G:I.24, G:I.24 Hydrogen bonds: E:I.110, E:D.111, E:D.111, E:I.112, E:N.227 SPH.3: 16 residues within 4Å: Chain I: I.110, D.111, I.112, F.134, F.136, Y.152, Y.154, V.189, V.191, Y.200, W.202, N.227, M.229, F.232, M.252 Chain K: I.24 23 PLIP interactions: 21 interactions with chain I, 2 interactions with chain K Hydrophobic interactions: I:I.110, I:I.110, I:I.112, I:F.134, I:F.134, I:F.136, I:Y.152, I:Y.154, I:Y.154, I:Y.154, I:V.189, I:V.191, I:V.191, I:Y.200, I:M.229, I:F.232, K:I.24, K:I.24 Hydrogen bonds: I:I.110, I:D.111, I:D.111, I:I.112, I:N.227 SPH.4: 16 residues within 4Å: Chain M: I.110, D.111, I.112, F.134, F.136, Y.152, Y.154, V.189, V.191, Y.200, W.202, N.227, M.229, F.232, M.252 Chain O: I.24 23 PLIP interactions: 21 interactions with chain M, 2 interactions with chain O Hydrophobic interactions: M:I.110, M:I.110, M:I.112, M:F.134, M:F.134, M:F.136, M:Y.152, M:Y.154, M:Y.154, M:Y.154, M:V.189, M:V.191, M:V.191, M:Y.200, M:M.229, M:F.232, O:I.24, O:I.24 Hydrogen bonds: M:I.110, M:D.111, M:D.111, M:I.112, M:N.227 SPH.5: 16 residues within 4Å: Chain Q: I.110, D.111, I.112, F.134, F.136, Y.152, Y.154, V.189, V.191, Y.200, W.202, N.227, M.229, F.232, M.252 Chain S: I.24 22 PLIP interactions: 20 interactions with chain Q, 2 interactions with chain S Hydrophobic interactions: Q:I.110, Q:I.110, Q:I.112, Q:F.134, Q:F.134, Q:F.136, Q:Y.152, Q:Y.154, Q:Y.154, Q:Y.154, Q:V.189, Q:V.191, Q:V.191, Q:Y.200, Q:M.229, Q:F.232, S:I.24, S:I.24 Hydrogen bonds: Q:I.110, Q:D.111, Q:I.112, Q:N.227 SPH.6: 16 residues within 4Å: Chain U: I.110, D.111, I.112, F.134, F.136, Y.152, Y.154, V.189, V.191, Y.200, W.202, N.227, M.229, F.232, M.252 Chain W: I.24 22 PLIP interactions: 20 interactions with chain U, 2 interactions with chain W Hydrophobic interactions: U:I.110, U:I.110, U:I.112, U:F.134, U:F.134, U:F.136, U:Y.152, U:Y.154, U:Y.154, U:Y.154, U:V.189, U:V.191, U:V.191, U:Y.200, U:M.229, U:F.232, W:I.24, W:I.24 Hydrogen bonds: U:I.110, U:D.111, U:I.112, U:N.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cui, Y. et al., Molecular basis of Coxsackievirus A10 entry using the two-in-one attachment and uncoating receptor KRM1. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-07-22

Peptides

Capsid protein VP1: AEIMQU
Capsid protein VP2: BFJNRV
Capsid protein VP3: CGKOSW
Capsid protein VP4: DHLPTX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

M
A

Q
A

U
A

B
B

F
B

J
B

N
B

R
B

V
B

C
C

G
C

K
C

O
C

S
C

W
C

D
D

H
D

L
D

P
D

T
D

X
D

Capsid protein VP1

Capsid protein VP2

Capsid protein VP3

Capsid protein VP4

Related Entries With Identical Sequence