SMTL ID : 3j8f.2 (3 other biounits)

Cryo-EM reconstruction of poliovirus-receptor complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.70 Å

Oligo State

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

Ligands

10 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 2 residues within 4Å: Chain E: V.95, N.105 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 5 residues within 4Å: Chain E: G.216, K.217, N.218, N.237 Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 2 residues within 4Å: Chain J: V.95, N.105 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 5 residues within 4Å: Chain J: G.216, K.217, N.218, N.237 Ligands: NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 2 residues within 4Å: Chain O: V.95, N.105 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 5 residues within 4Å: Chain O: G.216, K.217, N.218, N.237 Ligands: NAG-NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 2 residues within 4Å: Chain T: V.95, N.105 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 5 residues within 4Å: Chain T: G.216, K.217, N.218, N.237 Ligands: NAG-NAG.25 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 2 residues within 4Å: Chain Y: V.95, N.105 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.33: 5 residues within 4Å: Chain Y: G.216, K.217, N.218, N.237 Ligands: NAG-NAG.32 No protein-ligand interaction detected (PLIP)

5 x NAG- NAG- BMA- BMA- FUC: beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-FUC.2: 3 residues within 4Å: Chain E: G.119, N.120, W.138 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.120 NAG-NAG-BMA-BMA-FUC.9: 3 residues within 4Å: Chain J: G.119, N.120, W.138 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.120 NAG-NAG-BMA-BMA-FUC.16: 3 residues within 4Å: Chain O: G.119, N.120, W.138 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:N.120 NAG-NAG-BMA-BMA-FUC.23: 3 residues within 4Å: Chain T: G.119, N.120, W.138 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:N.120 NAG-NAG-BMA-BMA-FUC.30: 3 residues within 4Å: Chain Y: G.119, N.120, W.138 1 PLIP interactions: 1 interactions with chain Y Hydrogen bonds: Y:N.120

10 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 1 residues within 4Å: Chain E: N.188 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain E: N.218 Ligands: NAG-NAG-BMA.5 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain J: N.188 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain J: N.218 Ligands: NAG-NAG-BMA.12 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain O: N.188 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain O: N.218 Ligands: NAG-NAG-BMA.19 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 1 residues within 4Å: Chain T: N.188 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain T: N.218 Ligands: NAG-NAG-BMA.26 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 1 residues within 4Å: Chain Y: N.188 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 2 residues within 4Å: Chain Y: N.218 Ligands: NAG-NAG-BMA.33 No protein-ligand interaction detected (PLIP)

5 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.6: 3 residues within 4Å: Chain E: P.305, I.306, N.307 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.13: 3 residues within 4Å: Chain J: P.305, I.306, N.307 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.20: 3 residues within 4Å: Chain O: P.305, I.306, N.307 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.27: 3 residues within 4Å: Chain T: P.305, I.306, N.307 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.34: 3 residues within 4Å: Chain Y: P.305, I.306, N.307 No protein-ligand interaction detected (PLIP)

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

NAG.7: 3 residues within 4Å: Chain E: N.313, T.315, Q.322 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.313, E:T.315 NAG.14: 3 residues within 4Å: Chain J: N.313, T.315, Q.322 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:N.313, J:T.315 NAG.21: 3 residues within 4Å: Chain O: N.313, T.315, Q.322 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:N.313, O:T.315 NAG.28: 3 residues within 4Å: Chain T: N.313, T.315, Q.322 2 PLIP interactions: 2 interactions with chain T Hydrogen bonds: T:N.313, T:T.315 NAG.35: 3 residues within 4Å: Chain Y: N.313, T.315, Q.322 2 PLIP interactions: 2 interactions with chain Y Hydrogen bonds: Y:N.313, Y:T.315

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Strauss, M. et al., Nectin-Like Interactions between Poliovirus and Its Receptor Trigger Conformational Changes Associated with Cell Entry. J.Virol. (2015)

Release Date

2015-02-11

Peptides

Capsid protein VP1: AFKPU
Capsid protein VP2: BGLQV
Capsid protein VP3: CHMRW
Capsid protein VP4: DINSX
Poliovirus receptor: EJOTY

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

F
1

K
1

P
1

U
1

B
2

G
2

L
2

Q
2

V
2

C
3

H
3

M
3

R
3

W
3

D
4

I
4

N
4

S
4

X
4

E
7

J
7

O
7

T
7

Y
7

Capsid protein VP1

Capsid protein VP2

Capsid protein VP3

Capsid protein VP4

Poliovirus receptor

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