SMTL ID : 8tc0.1

Cryo-EM Structure of Spike Glycoprotein from Bat Coronavirus WIV1 in Closed Conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG-NAG-FUC.1: 4 residues within 4Å: Chain A: N.13, T.14, Q.15, N.48 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.14 NAG-NAG-FUC.5: 4 residues within 4Å: Chain A: D.250, E.251, N.252 Chain B: R.527 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.251 NAG-NAG-FUC.6: 5 residues within 4Å: Chain A: Y.672, N.674, G.1096 Chain C: L.759, D.761 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:N.674 Hydrogen bonds: C:D.761 NAG-NAG-FUC.9: 3 residues within 4Å: Chain A: N.301, K.549, T.550 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.12: 4 residues within 4Å: Chain B: N.13, T.14, Q.15, N.48 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.14 NAG-NAG-FUC.16: 4 residues within 4Å: Chain B: D.250, E.251, N.252 Chain C: R.527 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.251 NAG-NAG-FUC.17: 5 residues within 4Å: Chain A: L.759, D.761 Chain B: N.674, I.1095, G.1096 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.674 Hydrogen bonds: A:D.761 NAG-NAG-FUC.20: 3 residues within 4Å: Chain B: N.301, K.549, T.550 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.23: 4 residues within 4Å: Chain C: N.13, T.14, Q.15, N.48 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.14 NAG-NAG-FUC.27: 4 residues within 4Å: Chain A: R.527 Chain C: D.250, E.251, N.252 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.251 NAG-NAG-FUC.28: 5 residues within 4Å: Chain B: L.759, D.761 Chain C: N.674, I.1095, G.1096 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:N.674 Hydrogen bonds: B:D.761 NAG-NAG-FUC.31: 3 residues within 4Å: Chain C: N.301, K.549, T.550 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 7 residues within 4Å: Chain A: N.102, S.103, T.104, N.105, V.107, V.147, D.150 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 6 residues within 4Å: Chain B: N.102, S.103, T.104, N.105, V.107, V.147 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 7 residues within 4Å: Chain C: N.102, S.103, T.104, N.105, V.107, V.147, D.150 No protein-ligand interaction detected (PLIP)

9 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.3: 6 residues within 4Å: Chain A: N.112, F.140, N.141 Chain B: Y.321, A.322, I.438 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 10 residues within 4Å: Chain A: S.88, T.89, N.210, T.212 Chain B: R.427, H.428, L.431, R.432, D.446, G.447 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.446 NAG-NAG-BMA.7: 4 residues within 4Å: Chain A: D.761, N.766, S.768, Q.769 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 6 residues within 4Å: Chain B: N.112, F.140, N.141 Chain C: Y.321, A.322, I.438 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 10 residues within 4Å: Chain B: S.88, T.89, N.210, T.212 Chain C: R.427, H.428, L.431, R.432, D.446, G.447 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.446 NAG-NAG-BMA.18: 4 residues within 4Å: Chain B: D.761, N.766, S.768, Q.769 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 6 residues within 4Å: Chain A: Y.321, A.322, I.438 Chain C: N.112, F.140, N.141 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 10 residues within 4Å: Chain A: R.427, H.428, L.431, R.432, D.446, G.447 Chain C: S.88, T.89, N.210, T.212 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.446 NAG-NAG-BMA.29: 4 residues within 4Å: Chain C: D.761, N.766, S.768, Q.769 No protein-ligand interaction detected (PLIP)

9 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.8: 7 residues within 4Å: Chain A: N.91, N.92, E.114, L.115, D.117, N.138, F.140 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.91 Water bridges: A:N.92, A:N.92 NAG-NAG-BMA-FUC.10: 4 residues within 4Å: Chain A: N.585, T.587, Q.613 Chain C: M.799 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.11: 7 residues within 4Å: Chain A: N.682, S.684, Q.887, N.890, Q.891, Q.1036, F.1074 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.887, A:Q.891, A:Q.887 Hydrogen bonds: A:N.890 NAG-NAG-BMA-FUC.19: 7 residues within 4Å: Chain B: N.91, N.92, E.114, L.115, D.117, N.138, F.140 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.91 NAG-NAG-BMA-FUC.21: 4 residues within 4Å: Chain A: M.799 Chain B: N.585, T.587, Q.613 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.22: 8 residues within 4Å: Chain B: N.682, S.684, K.886, Q.887, N.890, Q.891, Q.1036, F.1074 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.887, B:Q.891 Hydrogen bonds: B:N.890 NAG-NAG-BMA-FUC.30: 7 residues within 4Å: Chain C: N.91, N.92, E.114, L.115, D.117, N.138, F.140 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.91 NAG-NAG-BMA-FUC.32: 4 residues within 4Å: Chain B: M.799 Chain C: N.585, T.587, Q.613 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.33: 7 residues within 4Å: Chain C: N.682, S.684, N.884, Q.887, Q.891, Q.1036, F.1074 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Q.891

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

NAG.34: 3 residues within 4Å: Chain A: N.340 Chain B: L.426, Y.458 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.340 Hydrophobic interactions: B:Y.458 NAG.35: 1 residues within 4Å: Chain A: N.313 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.313 NAG.36: 4 residues within 4Å: Chain A: R.1038, N.1063, G.1064, F.1068 No protein-ligand interaction detected (PLIP) NAG.37: 1 residues within 4Å: Chain A: N.1099 No protein-ligand interaction detected (PLIP) NAG.39: 3 residues within 4Å: Chain A: L.124, N.127, T.129 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.129 Hydrogen bonds: A:N.127 NAG.40: 3 residues within 4Å: Chain B: N.340 Chain C: L.426, Y.458 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.340 NAG.41: 1 residues within 4Å: Chain B: N.313 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.313 NAG.42: 4 residues within 4Å: Chain B: R.1038, N.1063, G.1064, F.1068 No protein-ligand interaction detected (PLIP) NAG.43: 1 residues within 4Å: Chain B: N.1099 No protein-ligand interaction detected (PLIP) NAG.45: 5 residues within 4Å: Chain B: L.124, S.126, N.127, T.129, I.131 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.129 Hydrogen bonds: B:N.127 NAG.46: 3 residues within 4Å: Chain A: L.426, Y.458 Chain C: N.340 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.340 NAG.47: 1 residues within 4Å: Chain C: N.313 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.313 NAG.48: 4 residues within 4Å: Chain C: R.1038, N.1063, G.1064, F.1068 No protein-ligand interaction detected (PLIP) NAG.49: 1 residues within 4Å: Chain C: N.1099 No protein-ligand interaction detected (PLIP) NAG.51: 4 residues within 4Å: Chain C: L.124, N.127, T.129, I.131 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.127

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.38: 24 residues within 4Å: Chain A: C.306, P.307, F.308, V.311, F.312, I.328, A.333, Y.335, L.338, Y.339, F.344, F.347, L.357, F.362, V.365, A.367, C.402, L.404, L.482, F.484, V.493 Chain B: R.378, T.385, G.386 18 PLIP interactions: 2 interactions with chain B, 16 interactions with chain A Hydrogen bonds: B:T.385 Salt bridges: B:R.378 Hydrophobic interactions: A:F.308, A:I.328, A:A.333, A:Y.335, A:L.338, A:Y.339, A:F.347, A:L.357, A:F.362, A:F.362, A:V.365, A:L.404, A:L.482, A:L.482, A:F.484, A:V.493 EIC.44: 24 residues within 4Å: Chain B: C.306, P.307, F.308, V.311, F.312, I.328, A.333, Y.335, L.338, Y.339, F.344, F.347, L.357, F.362, V.365, A.367, C.402, L.404, L.482, F.484, V.493 Chain C: R.378, T.385, G.386 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.308, B:I.328, B:A.333, B:Y.335, B:Y.335, B:L.338, B:Y.339, B:F.347, B:L.357, B:F.362, B:F.362, B:L.404, B:L.482, B:L.482, B:F.484, B:V.493 Hydrogen bonds: C:T.385 Salt bridges: C:R.378 EIC.50: 24 residues within 4Å: Chain A: R.378, T.385, G.386 Chain C: C.306, P.307, F.308, V.311, F.312, I.328, A.333, Y.335, L.338, Y.339, F.344, F.347, L.357, F.362, V.365, A.367, C.402, L.404, L.482, F.484, V.493 19 PLIP interactions: 16 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:F.308, C:I.328, C:A.333, C:Y.335, C:L.338, C:Y.339, C:F.347, C:F.347, C:L.357, C:F.362, C:F.362, C:L.404, C:L.482, C:L.482, C:F.484, C:V.493 Hydrogen bonds: A:T.385 Water bridges: A:V.387 Salt bridges: A:R.378

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hills, F.R. et al., Variation in structural motifs within SARS-related coronavirus spike proteins. Plos Pathog. (2024)

Release Date

2024-05-01

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein