SMTL ID : 6la3.2 (3 other biounits)

Cryo-EM structure of full echovirus 11 particle at pH 7.4

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-5-5-5-mer

Ligands

5 x SPH: SPHINGOSINE(Non-covalent)

SPH.1: 16 residues within 4Å: Chain A: I.93, A.95, M.115, I.142, Y.144, P.166, S.167, I.168, M.179, I.181, I.184, Y.190, N.192, M.214, I.217, M.236 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.93, A:Y.144, A:I.168, A:I.181, A:I.184, A:I.217 Hydrogen bonds: A:N.192 SPH.2: 16 residues within 4Å: Chain E: I.93, A.95, M.115, I.142, Y.144, P.166, S.167, I.168, M.179, I.181, I.184, Y.190, N.192, M.214, I.217, M.236 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:I.93, E:Y.144, E:I.168, E:I.181, E:I.184, E:I.217 Hydrogen bonds: E:N.192 SPH.3: 16 residues within 4Å: Chain I: I.93, A.95, M.115, I.142, Y.144, P.166, S.167, I.168, M.179, I.181, I.184, Y.190, N.192, M.214, I.217, M.236 7 PLIP interactions: 7 interactions with chain I Hydrophobic interactions: I:I.93, I:Y.144, I:I.168, I:I.181, I:I.184, I:I.217 Hydrogen bonds: I:N.192 SPH.4: 16 residues within 4Å: Chain M: I.93, A.95, M.115, I.142, Y.144, P.166, S.167, I.168, M.179, I.181, I.184, Y.190, N.192, M.214, I.217, M.236 7 PLIP interactions: 7 interactions with chain M Hydrophobic interactions: M:I.93, M:Y.144, M:I.168, M:I.181, M:I.184, M:I.217 Hydrogen bonds: M:N.192 SPH.5: 16 residues within 4Å: Chain Q: I.93, A.95, M.115, I.142, Y.144, P.166, S.167, I.168, M.179, I.181, I.184, Y.190, N.192, M.214, I.217, M.236 7 PLIP interactions: 7 interactions with chain Q Hydrophobic interactions: Q:I.93, Q:Y.144, Q:I.168, Q:I.181, Q:I.184, Q:I.217 Hydrogen bonds: Q:N.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niu, S. et al., Molecular and structural basis of Echovirus 11 infection by using the dual-receptor system of CD55 and FcRn. Chin.Sci.Bull. (2020)

Release Date

2020-10-07

Peptides

Capsid protein VP1: AEIMQ
Capsid protein VP2: BFJNR
Capsid protein VP3: CGKOS
Capsid protein VP4: DHLPT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

M
A

Q
A

B
B

F
B

J
B

N
B

R
B

C
C

G
C

K
C

O
C

S
C

D
D

H
D

L
D

P
D

T
D

Capsid protein VP1

Capsid protein VP2

Capsid protein VP3

Capsid protein VP4

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