SMTL ID : 9cri.1

Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Mu (B.1.621) variant 3 closed RBDs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

27 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: 6 residues within 4Å: Chain A: N.122, A.123, T.124, N.125, V.127, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: E.132, N.164, N.165 Chain B: Y.351, A.352, I.468 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.468 NAG-NAG.3: 7 residues within 4Å: Chain A: T.108, N.234, T.236 Chain B: R.457, S.459, K.462, E.465 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.462 NAG-NAG.4: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain B: K.558 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain A: N.717, F.718, T.719, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.7: 5 residues within 4Å: Chain A: N.801, S.803, Q.804, F.817, Q.935 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.1101 NAG-NAG.10: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 7 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, V.127, E.169, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: E.132, N.164, N.165 Chain C: I.468 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 8 residues within 4Å: Chain B: T.108, N.234 Chain C: R.457, S.459, L.461, K.462, E.465, R.466 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.457, C:R.457, C:S.459, C:E.465, C:E.465 NAG-NAG.14: 4 residues within 4Å: Chain B: N.280, E.281, N.282 Chain C: K.558 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain B: N.616, T.618, E.619, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 7 residues within 4Å: Chain B: N.717, F.718, T.719, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.17: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain B: N.1098, G.1099, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.1101 NAG-NAG.20: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 7 residues within 4Å: Chain C: N.122, A.123, T.124, N.125, V.127, E.169, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain A: Y.351, I.468 Chain C: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 7 residues within 4Å: Chain A: R.457, K.458, S.459, K.462, E.465 Chain C: T.108, N.234 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.459, A:K.462 NAG-NAG.24: 4 residues within 4Å: Chain A: K.558 Chain C: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain C: N.616, T.618, E.619, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 6 residues within 4Å: Chain C: N.717, T.719, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.27: 5 residues within 4Å: Chain C: N.801, S.803, Q.804, F.817, Q.935 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 5 residues within 4Å: Chain C: N.1098, G.1099, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.1101 NAG-NAG.30: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

3 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.8: 6 residues within 4Å: Chain A: A.706, A.713, E.1072, K.1073, N.1074 Chain C: Q.895 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.18: 6 residues within 4Å: Chain A: Q.895 Chain B: S.704, A.706, E.1072, K.1073, N.1074 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.706, B:N.1074 NAG-NAG-FUC.28: 6 residues within 4Å: Chain B: Q.895 Chain C: A.706, A.713, E.1072, K.1073, N.1074 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1074

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

NAG.31: 4 residues within 4Å: Chain A: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: R.328, N.331, Q.580, T.581 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: G.339, F.342, N.343 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain A: N.709, N.710, P.1079, I.1130, G.1131 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain B: R.328, N.331, Q.580, T.581 Ligand excluded by PLIP NAG.39: 6 residues within 4Å: Chain B: F.338, G.339, F.342, N.343, L.368, F.374 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.42: 6 residues within 4Å: Chain A: D.796 Chain B: N.709, N.710, P.1079, I.1130, G.1131 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: R.328, N.331, Q.580, T.581 Ligand excluded by PLIP NAG.45: 6 residues within 4Å: Chain C: F.338, G.339, F.342, N.343, L.368, F.374 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain C: E.654, H.655, V.656, N.657 Ligand excluded by PLIP NAG.48: 6 residues within 4Å: Chain B: D.796 Chain C: N.709, N.710, P.1079, I.1130, G.1131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ke, Z. et al., Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants. Embo J. (2024)

Release Date

2024-11-27

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

Spike glycoprotein