SMTL ID : 8wq0.1

Cryo-EM structure of WIV1 spike glycoprotein (the closed state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

26 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: 2 residues within 4Å: Chain A: Q.33, N.66 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.603, T.605, Q.631 Chain B: M.817 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1081, T.1083, S.1084, F.1086 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1117 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: N.110, E.132, N.156, F.158 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 9 residues within 4Å: Chain A: S.106, N.228, T.230 Chain C: R.445, H.446, G.447, K.448, R.450, E.453 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: D.268, E.269, N.270 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain A: T.699, N.700, Q.905, N.908, Q.909, Q.1054 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.908 Hydrogen bonds: A:Q.909 NAG-NAG.11: 3 residues within 4Å: Chain A: N.319, K.567, T.568 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain B: Q.33, N.66 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: N.110, E.132, N.156, F.158 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain B: N.319, K.567 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain B: N.1117 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain B: D.779, N.784, S.786, Q.787 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 7 residues within 4Å: Chain A: R.445, H.446, G.447, K.448, E.453 Chain B: N.228, T.230 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain A: R.545 Chain B: D.268, E.269, N.270 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain B: N.603, T.605 Chain C: Q.819 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain C: Q.33, N.66 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain C: N.110, E.132, N.156, F.158 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 6 residues within 4Å: Chain B: R.445, H.446, E.453 Chain C: S.106, N.228, T.230 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain B: R.545 Chain C: D.268, E.269, N.270 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain C: N.319, K.567, T.568 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 2 residues within 4Å: Chain C: N.692, G.1114 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 3 residues within 4Å: Chain C: A.689, E.1055, N.1057 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain C: N.1081, T.1083, S.1084, F.1086 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 1 residues within 4Å: Chain C: N.1117 No protein-ligand interaction detected (PLIP)

7 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.2: 6 residues within 4Å: Chain A: N.120, S.121, T.122, N.123, V.125, V.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.123 NAG-NAG-BMA.6: 4 residues within 4Å: Chain A: D.779, N.784, S.786, Q.787 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 6 residues within 4Å: Chain B: N.120, S.121, T.122, N.123, V.125, D.168 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 5 residues within 4Å: Chain B: T.699, N.700, Q.905, Q.909, Q.1054 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 5 residues within 4Å: Chain C: N.120, S.121, T.122, N.123, V.125 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.123 NAG-NAG-BMA.29: 5 residues within 4Å: Chain C: T.699, N.700, Q.905, Q.909, Q.1054 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.33: 4 residues within 4Å: Chain C: D.779, N.784, S.786, Q.787 No protein-ligand interaction detected (PLIP)

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

NAG.34: 3 residues within 4Å: Chain A: N.331, S.359, T.360 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: E.295, N.590 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.358 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: L.142, N.145, T.147 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.692 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain A: A.689, E.1055, R.1056, N.1057 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain A: F.158, N.159 Chain C: Y.339 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: L.142, N.145, T.147 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: N.331, S.359 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.590 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.358 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.692 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain B: A.689, E.1055, R.1056, N.1057 Chain C: Q.878 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain A: Y.339, I.456 Chain B: F.158, N.159 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain B: N.1081, T.1083, F.1086, P.1095 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: L.142, N.145, T.147 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.331, S.359 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: E.295, N.590 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.358 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain A: Q.819 Chain C: N.603 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain B: Y.339, I.456 Chain C: F.158, N.159 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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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