SMTL ID : 7yrh.2 (3 other biounits)

Cryo-EM structure of compact coxsackievirus A16 empty particle in complex with a neutralizing antibody 9B5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-5-5-5-5-mer

Ligands

5 x SPH: SPHINGOSINE(Non-covalent)

SPH.1: 16 residues within 4Å: Chain A: I.111, D.112, L.113, F.131, F.135, F.137, Y.153, Y.155, V.190, V.192, W.203, N.228, M.230, F.233, M.253 Chain C: I.24 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.111, A:I.111, A:L.113, A:L.113, A:F.131, A:F.135, A:F.135, A:F.135, A:F.137, A:Y.153, A:Y.155, A:Y.155, A:V.190, A:V.192 Hydrogen bonds: A:D.112, A:D.112, A:L.113, A:N.228 SPH.2: 16 residues within 4Å: Chain F: I.111, D.112, L.113, F.131, F.135, F.137, Y.153, Y.155, V.190, V.192, W.203, N.228, M.230, F.233, M.253 Chain H: I.24 18 PLIP interactions: 18 interactions with chain F Hydrophobic interactions: F:I.111, F:I.111, F:L.113, F:L.113, F:F.131, F:F.135, F:F.135, F:F.135, F:F.137, F:Y.153, F:Y.155, F:Y.155, F:V.190, F:V.192 Hydrogen bonds: F:D.112, F:D.112, F:L.113, F:N.228 SPH.3: 16 residues within 4Å: Chain K: I.111, D.112, L.113, F.131, F.135, F.137, Y.153, Y.155, V.190, V.192, W.203, N.228, M.230, F.233, M.253 Chain M: I.24 18 PLIP interactions: 18 interactions with chain K Hydrophobic interactions: K:I.111, K:I.111, K:L.113, K:L.113, K:F.131, K:F.135, K:F.135, K:F.135, K:F.137, K:Y.153, K:Y.155, K:Y.155, K:V.190, K:V.192 Hydrogen bonds: K:D.112, K:D.112, K:L.113, K:N.228 SPH.4: 16 residues within 4Å: Chain P: I.111, D.112, L.113, F.131, F.135, F.137, Y.153, Y.155, V.190, V.192, W.203, N.228, M.230, F.233, M.253 Chain R: I.24 18 PLIP interactions: 18 interactions with chain P Hydrophobic interactions: P:I.111, P:I.111, P:L.113, P:L.113, P:F.131, P:F.135, P:F.135, P:F.135, P:F.137, P:Y.153, P:Y.155, P:Y.155, P:V.190, P:V.192 Hydrogen bonds: P:D.112, P:D.112, P:L.113, P:N.228 SPH.5: 16 residues within 4Å: Chain U: I.111, D.112, L.113, F.131, F.135, F.137, Y.153, Y.155, V.190, V.192, W.203, N.228, M.230, F.233, M.253 Chain W: I.24 18 PLIP interactions: 18 interactions with chain U Hydrophobic interactions: U:I.111, U:I.111, U:L.113, U:L.113, U:F.131, U:F.135, U:F.135, U:F.135, U:F.137, U:Y.153, U:Y.155, U:Y.155, U:V.190, U:V.192 Hydrogen bonds: U:D.112, U:D.112, U:L.113, U:N.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, C. et al., Molecular mechanism of antibody neutralization of coxsackievirus A16. Nat Commun (2022)

Release Date

2022-09-14

Peptides

Capsid protein VP1: AFKPU
Genome polyprotein: BGLQV
Capsid protein VP3: CHMRW
The light chain of the antibody 9B5: DINSX
The heavy chain of the antibody 9B5: EJOTY

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
A

K
A

P
A

U
A

B
B

G
B

L
B

Q
B

V
B

C
C

H
C

M
C

R
C

W
C

D
E

I
E

N
E

S
E

X
E

E
F

J
F

O
F

T
F

Y
F

Capsid protein VP1

Genome polyprotein

Capsid protein VP3

The light chain of the antibody 9B5

The heavy chain of the antibody 9B5

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