SMTL ID : 7dq7.3 (3 other biounits)

Cryo-EM structure of Coxsackievirus B1 mature virion in complex with nAb 5F5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-6-6-6-6-mer

Ligands

12 x PLM: PALMITIC ACID(Non-covalent)

PLM.1: 11 residues within 4Å: Chain A: I.92, T.94, R.95, L.114, L.116, Y.143, I.180, I.183, S.190, C.191 Ligands: PLM.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.92, A:I.92, A:T.94, A:L.114, A:L.116, A:Y.143, A:I.180, A:I.183 Salt bridges: A:R.95 PLM.2: 2 residues within 4Å: Chain A: I.180 Ligands: PLM.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.180 PLM.3: 11 residues within 4Å: Chain G: I.92, T.94, R.95, L.114, L.116, Y.143, I.180, I.183, S.190, C.191 Ligands: PLM.4 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:I.92, G:I.92, G:T.94, G:L.114, G:L.116, G:Y.143, G:I.180, G:I.183 Salt bridges: G:R.95 PLM.4: 2 residues within 4Å: Chain G: I.180 Ligands: PLM.3 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:I.180 PLM.5: 11 residues within 4Å: Chain M: I.92, T.94, R.95, L.114, L.116, Y.143, I.180, I.183, S.190, C.191 Ligands: PLM.6 9 PLIP interactions: 9 interactions with chain M Hydrophobic interactions: M:I.92, M:I.92, M:T.94, M:L.114, M:L.116, M:Y.143, M:I.180, M:I.183 Salt bridges: M:R.95 PLM.6: 2 residues within 4Å: Chain M: I.180 Ligands: PLM.5 1 PLIP interactions: 1 interactions with chain M Hydrophobic interactions: M:I.180 PLM.7: 11 residues within 4Å: Chain S: I.92, T.94, R.95, L.114, L.116, Y.143, I.180, I.183, S.190, C.191 Ligands: PLM.8 9 PLIP interactions: 9 interactions with chain S Hydrophobic interactions: S:I.92, S:I.92, S:T.94, S:L.114, S:L.116, S:Y.143, S:I.180, S:I.183 Salt bridges: S:R.95 PLM.8: 2 residues within 4Å: Chain S: I.180 Ligands: PLM.7 1 PLIP interactions: 1 interactions with chain S Hydrophobic interactions: S:I.180 PLM.9: 11 residues within 4Å: Chain Y: I.92, T.94, R.95, L.114, L.116, Y.143, I.180, I.183, S.190, C.191 Ligands: PLM.10 9 PLIP interactions: 9 interactions with chain Y Hydrophobic interactions: Y:I.92, Y:I.92, Y:T.94, Y:L.114, Y:L.116, Y:Y.143, Y:I.180, Y:I.183 Salt bridges: Y:R.95 PLM.10: 2 residues within 4Å: Chain Y: I.180 Ligands: PLM.9 1 PLIP interactions: 1 interactions with chain Y Hydrophobic interactions: Y:I.180 PLM.11: 11 residues within 4Å: Chain 4: I.92, T.94, R.95, L.114, L.116, Y.143, I.180, I.183, S.190, C.191 Ligands: PLM.12 9 PLIP interactions: 9 interactions with chain 4 Hydrophobic interactions: 4:I.92, 4:I.92, 4:T.94, 4:L.114, 4:L.116, 4:Y.143, 4:I.180, 4:I.183 Salt bridges: 4:R.95 PLM.12: 2 residues within 4Å: Chain 4: I.180 Ligands: PLM.11 1 PLIP interactions: 1 interactions with chain 4 Hydrophobic interactions: 4:I.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, L. et al., Cryo-EM structures reveal the molecular basis of receptor-initiated coxsackievirus uncoating. Cell Host Microbe (2021)

Release Date

2021-05-05

Peptides

Virion protein 1: AGMSY4
VP2: BHNTZ5
VP3: CIOU06
Capsid protein VP4: DJPV17
5F5 VL: EKQW28
5F5 VH: FLRX39

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
A

M
A

S
A

Y
A

4
A

B
B

H
B

N
B

T
B

Z
B

5
B

C
C

I
C

O
C

U
C

0
C

6
C

D
D

J
D

P
D

V
D

1
D

7
D

E
L

K
L

Q
L

W
L

2
L

8
L

F
H

L
H

R
H

X
H

3
H

9
H

Virion protein 1

VP2

VP3

Capsid protein VP4

5F5 VL

5F5 VH

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