SMTL ID : 8wly.1

Cryo-EM structure of bat WIV1 spike glycoprotein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG-NAG.1: 4 residues within 4Å: Chain A: N.700, Q.905, Q.909, Q.1054 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.909 NAG-NAG.2: 3 residues within 4Å: Chain A: N.1081, T.1083, F.1086 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.1117 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: D.779, N.784, S.786, Q.787 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: M.118, N.120, T.122, N.123, D.168 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.331, S.359, T.360 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: D.297, G.588, N.590, T.591 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.1081, T.1083, F.1086 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain A: R.545 Chain B: D.268, E.269, N.270 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: R.545 Chain C: E.269, N.270 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.545 NAG-NAG.13: 5 residues within 4Å: Chain C: T.699, N.700, K.904, K.912, Q.1054 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.904 NAG-NAG.15: 3 residues within 4Å: Chain C: N.1081, T.1083, F.1086 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain C: N.1117 No protein-ligand interaction detected (PLIP)

3 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.8: 4 residues within 4Å: Chain B: N.700, Q.905, Q.909, Q.1054 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 4 residues within 4Å: Chain B: D.779, N.784, S.786, Q.787 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 4 residues within 4Å: Chain C: D.779, N.784, S.786, Q.787 No protein-ligand interaction detected (PLIP)

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

NAG.17: 4 residues within 4Å: Chain A: D.268, E.269, N.270 Chain C: R.545 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.603, T.605 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.692 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.1057 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: D.64, N.66 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.603, Q.631 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.692 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.1057 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.1117 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.319, P.566, K.567 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.66 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: N.110, E.132, F.158 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: F.158, N.159 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: R.450 Chain C: S.106, N.228, T.230 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.590 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.692 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: Q.878 Chain C: N.1057 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain C: N.120, S.121, N.123, V.125, Q.148 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qiao, S. et al., Structural determinants of spike infectivity in bat SARS-like coronaviruses RsSHC014 and WIV1. J.Virol. (2024)

Release Date

2024-07-17

Peptides

Spike glycoprotein,Fibritin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein,Fibritin

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