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

Cryo-EM structure of mature Coxsackievirus A10 in complex with KRM1 at pH 7.4

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

6 x SPH: SPHINGOSINE(Non-covalent)

SPH.1: 13 residues within 4Å: Chain A: I.110, D.111, I.112, M.113, F.134, F.136, Y.154, V.191, Y.200, W.202, N.227, M.229, F.232 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.110, A:I.112, A:F.134, A:F.136, A:Y.154, A:Y.154, A:Y.154, A:V.191, A:V.191, A:M.229, A:F.232, A:F.232 Hydrogen bonds: A:I.110, A:I.112, A:N.227 SPH.5: 13 residues within 4Å: Chain F: I.110, D.111, I.112, M.113, F.134, F.136, Y.154, V.191, Y.200, W.202, N.227, M.229, F.232 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:I.110, F:I.112, F:F.134, F:F.136, F:Y.154, F:Y.154, F:Y.154, F:V.191, F:V.191, F:M.229, F:F.232, F:F.232 Hydrogen bonds: F:I.110, F:I.112, F:N.227 SPH.9: 13 residues within 4Å: Chain K: I.110, D.111, I.112, M.113, F.134, F.136, Y.154, V.191, Y.200, W.202, N.227, M.229, F.232 15 PLIP interactions: 15 interactions with chain K Hydrophobic interactions: K:I.110, K:I.112, K:F.134, K:F.136, K:Y.154, K:Y.154, K:Y.154, K:V.191, K:V.191, K:M.229, K:F.232, K:F.232 Hydrogen bonds: K:I.110, K:I.112, K:N.227 SPH.13: 13 residues within 4Å: Chain P: I.110, D.111, I.112, M.113, F.134, F.136, Y.154, V.191, Y.200, W.202, N.227, M.229, F.232 15 PLIP interactions: 15 interactions with chain P Hydrophobic interactions: P:I.110, P:I.112, P:F.134, P:F.136, P:Y.154, P:Y.154, P:Y.154, P:V.191, P:V.191, P:M.229, P:F.232, P:F.232 Hydrogen bonds: P:I.110, P:I.112, P:N.227 SPH.17: 13 residues within 4Å: Chain U: I.110, D.111, I.112, M.113, F.134, F.136, Y.154, V.191, Y.200, W.202, N.227, M.229, F.232 15 PLIP interactions: 15 interactions with chain U Hydrophobic interactions: U:I.110, U:I.112, U:F.134, U:F.136, U:Y.154, U:Y.154, U:Y.154, U:V.191, U:V.191, U:M.229, U:F.232, U:F.232 Hydrogen bonds: U:I.110, U:I.112, U:N.227 SPH.21: 13 residues within 4Å: Chain Z: I.110, D.111, I.112, M.113, F.134, F.136, Y.154, V.191, Y.200, W.202, N.227, M.229, F.232 15 PLIP interactions: 15 interactions with chain Z Hydrophobic interactions: Z:I.110, Z:I.112, Z:F.134, Z:F.136, Z:Y.154, Z:Y.154, Z:Y.154, Z:V.191, Z:V.191, Z:M.229, Z:F.232, Z:F.232 Hydrogen bonds: Z:I.110, Z:I.112, Z:N.227

18 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 3 residues within 4Å: Chain E: N.25, W.26, N.62 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain E: N.39, E.40, E.60 Ligand excluded by PLIP NAG.4: 5 residues within 4Å: Chain E: H.231, H.233, S.271, F.272, N.273 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain J: N.25, W.26, N.62 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain J: N.39, E.40, E.60 Ligand excluded by PLIP NAG.8: 5 residues within 4Å: Chain J: H.231, H.233, S.271, F.272, N.273 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain O: N.25, W.26, N.62 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain O: N.39, E.40, E.60 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain O: H.231, H.233, S.271, F.272, N.273 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain T: N.25, W.26, N.62 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain T: N.39, E.40, E.60 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain T: H.231, H.233, S.271, F.272, N.273 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain Y: N.25, W.26, N.62 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain Y: N.39, E.40, E.60 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain Y: H.231, H.233, S.271, F.272, N.273 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain 3: N.25, W.26, N.62 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain 3: N.39, E.40, E.60 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain 3: H.231, H.233, S.271, F.272, N.273 Ligand excluded by PLIP

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: AFKPUZ
Capsid protein VP2: BGLQV0
Capsid protein VP3: CHMRW1
Capsid protein VP4: DINSX2
KRM1: EJOTY3

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
A

K
A

P
A

U
A

Z
A

B
B

G
B

L
B

Q
B

V
B

0
B

C
C

H
C

M
C

R
C

W
C

1
C

D
D

I
D

N
D

S
D

X
D

2
D

E
E

J
E

O
E

T
E

Y
E

3
E

Capsid protein VP1

Capsid protein VP2

Capsid protein VP3

Capsid protein VP4

KRM1

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