SMTL ID : 4c10.2 (3 other biounits)

Cryo-EM reconstruction of empty enterovirus 71 in complex with a neutralizing antibody E19

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 13.00 Å

Oligo State

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

Ligands

5 x SPH: SPHINGOSINE(Non-covalent)

SPH.1: 11 residues within 4Å: Chain C: I.111, D.112, F.135, Y.153, F.155, V.179, V.192, Y.201, W.203, N.228, F.233 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:I.111, C:F.135, C:F.135, C:Y.153, C:F.155, C:V.179, C:V.192, C:V.192, C:W.203, C:F.233 Hydrogen bonds: C:I.111, C:D.112, C:Q.202 SPH.9: 11 residues within 4Å: Chain I: I.111, D.112, F.135, Y.153, F.155, V.179, V.192, Y.201, W.203, N.228, F.233 13 PLIP interactions: 13 interactions with chain I Hydrophobic interactions: I:I.111, I:F.135, I:F.135, I:Y.153, I:F.155, I:V.179, I:V.192, I:V.192, I:W.203, I:F.233 Hydrogen bonds: I:I.111, I:D.112, I:Q.202 SPH.17: 11 residues within 4Å: Chain O: I.111, D.112, F.135, Y.153, F.155, V.179, V.192, Y.201, W.203, N.228, F.233 13 PLIP interactions: 13 interactions with chain O Hydrophobic interactions: O:I.111, O:F.135, O:F.135, O:Y.153, O:F.155, O:V.179, O:V.192, O:V.192, O:W.203, O:F.233 Hydrogen bonds: O:I.111, O:D.112, O:Q.202 SPH.25: 11 residues within 4Å: Chain U: I.111, D.112, F.135, Y.153, F.155, V.179, V.192, Y.201, W.203, N.228, F.233 13 PLIP interactions: 13 interactions with chain U Hydrophobic interactions: U:I.111, U:F.135, U:F.135, U:Y.153, U:F.155, U:V.179, U:V.192, U:V.192, U:W.203, U:F.233 Hydrogen bonds: U:I.111, U:D.112, U:Q.202 SPH.33: 11 residues within 4Å: Chain 0: I.111, D.112, F.135, Y.153, F.155, V.179, V.192, Y.201, W.203, N.228, F.233 13 PLIP interactions: 13 interactions with chain 0 Hydrophobic interactions: 0:I.111, 0:F.135, 0:F.135, 0:Y.153, 0:F.155, 0:V.179, 0:V.192, 0:V.192, 0:W.203, 0:F.233 Hydrogen bonds: 0:I.111, 0:D.112, 0:Q.202

30 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain C: T.28, G.29, N.31, N.71 Ligand excluded by PLIP NA.3: 4 residues within 4Å: Chain C: S.56, T.58 Chain E: E.116, Q.221 Ligand excluded by PLIP NA.4: 7 residues within 4Å: Chain C: V.44, P.45, L.47, Q.48 Chain F: E.63, A.65, P.67 Ligand excluded by PLIP NA.5: 3 residues within 4Å: Chain C: E.164, S.165, S.168 Ligand excluded by PLIP NA.6: 5 residues within 4Å: Chain C: S.15, S.17 Chain D: S.40, Y.41, R.103 Ligand excluded by PLIP NA.7: 6 residues within 4Å: Chain C: Q.189 Chain E: V.20, S.21 Chain K: P.8 Chain Q: E.5 Chain W: G.1 Ligand excluded by PLIP NA.10: 4 residues within 4Å: Chain I: T.28, G.29, N.31, N.71 Ligand excluded by PLIP NA.11: 4 residues within 4Å: Chain I: S.56, T.58 Chain K: E.116, Q.221 Ligand excluded by PLIP NA.12: 7 residues within 4Å: Chain I: V.44, P.45, L.47, Q.48 Chain L: E.63, A.65, P.67 Ligand excluded by PLIP NA.13: 3 residues within 4Å: Chain I: E.164, S.165, S.168 Ligand excluded by PLIP NA.14: 5 residues within 4Å: Chain I: S.15, S.17 Chain J: S.40, Y.41, R.103 Ligand excluded by PLIP NA.15: 6 residues within 4Å: Chain 2: G.1 Chain I: Q.189 Chain K: V.20, S.21 Chain Q: P.8 Chain W: E.5 Ligand excluded by PLIP NA.18: 4 residues within 4Å: Chain O: T.28, G.29, N.31, N.71 Ligand excluded by PLIP NA.19: 4 residues within 4Å: Chain O: S.56, T.58 Chain Q: E.116, Q.221 Ligand excluded by PLIP NA.20: 7 residues within 4Å: Chain O: V.44, P.45, L.47, Q.48 Chain R: E.63, A.65, P.67 Ligand excluded by PLIP NA.21: 3 residues within 4Å: Chain O: E.164, S.165, S.168 Ligand excluded by PLIP NA.22: 5 residues within 4Å: Chain O: S.15, S.17 Chain P: S.40, Y.41, R.103 Ligand excluded by PLIP NA.23: 6 residues within 4Å: Chain 2: E.5 Chain E: G.1 Chain O: Q.189 Chain Q: V.20, S.21 Chain W: P.8 Ligand excluded by PLIP NA.26: 4 residues within 4Å: Chain U: T.28, G.29, N.31, N.71 Ligand excluded by PLIP NA.27: 4 residues within 4Å: Chain U: S.56, T.58 Chain W: E.116, Q.221 Ligand excluded by PLIP NA.28: 7 residues within 4Å: Chain U: V.44, P.45, L.47, Q.48 Chain X: E.63, A.65, P.67 Ligand excluded by PLIP NA.29: 3 residues within 4Å: Chain U: E.164, S.165, S.168 Ligand excluded by PLIP NA.30: 5 residues within 4Å: Chain U: S.15, S.17 Chain V: S.40, Y.41, R.103 Ligand excluded by PLIP NA.31: 6 residues within 4Å: Chain 2: P.8 Chain E: E.5 Chain K: G.1 Chain U: Q.189 Chain W: V.20, S.21 Ligand excluded by PLIP NA.34: 4 residues within 4Å: Chain 0: T.28, G.29, N.31, N.71 Ligand excluded by PLIP NA.35: 4 residues within 4Å: Chain 0: S.56, T.58 Chain 2: E.116, Q.221 Ligand excluded by PLIP NA.36: 7 residues within 4Å: Chain 0: V.44, P.45, L.47, Q.48 Chain 3: E.63, A.65, P.67 Ligand excluded by PLIP NA.37: 3 residues within 4Å: Chain 0: E.164, S.165, S.168 Ligand excluded by PLIP NA.38: 5 residues within 4Å: Chain 0: S.15, S.17 Chain 1: S.40, Y.41, R.103 Ligand excluded by PLIP NA.39: 6 residues within 4Å: Chain 0: Q.189 Chain 2: V.20, S.21 Chain E: P.8 Chain K: E.5 Chain Q: G.1 Ligand excluded by PLIP

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 6 residues within 4Å: Chain E: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain K: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.24: 6 residues within 4Å: Chain Q: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.32: 6 residues within 4Å: Chain W: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP CL.40: 6 residues within 4Å: Chain 2: D.89, P.90, G.91, W.111, H.180, A.181 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Plevka, P. et al., Neutralizing Antibodies Can Initiate Genome Release from Human Enterovirus 71. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-02-05

Peptides

EV19 5 C1-6 F1 C11: AGMSY
EV19 5 C1-6 F1 C11: BHNTZ
VP1: CIOU0
VP3: DJPV1
VP2: EKQW2
VP4: FLRX3

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
4

G
4

M
4

S
4

Y
4

B
5

H
5

N
5

T
5

Z
5

C
A

I
A

O
A

U
A

0
A

D
B

J
B

P
B

V
B

1
B

E
C

K
C

Q
C

W
C

2
C

F
D

L
D

R
D

X
D

3
D

EV19 5 C1-6 F1 C11

EV19 5 C1-6 F1 C11

VP1

VP3

VP2

VP4

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