SMTL ID : 9crg.1

Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Gamma (P.1) 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: 7 residues within 4Å: Chain A: N.122, A.123, T.124, N.125, V.127, E.169, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: E.132, N.164, N.165 Chain C: I.468 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain C: 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: 6 residues within 4Å: Chain A: N.717, T.719, L.922, N.925, Q.926, Q.1071 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.925 Hydrogen bonds: A:N.925 NAG-NAG.7: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 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: 2 residues within 4Å: Chain A: G.1085, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 8 residues within 4Å: Chain C: N.122, A.123, T.124, N.125, V.127, K.129, E.169, V.171 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.171 NAG-NAG.12: 4 residues within 4Å: Chain B: I.468 Chain C: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: E.465 Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: K.558 Chain C: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 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.17: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 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.20: 2 residues within 4Å: Chain C: G.1085, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 8 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, V.127, K.129, E.169, V.171 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171 NAG-NAG.22: 4 residues within 4Å: Chain A: I.468 Chain B: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain A: E.465 Chain B: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain A: K.558 Chain B: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 6 residues within 4Å: Chain B: N.717, T.719, L.922, N.925, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 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.30: 1 residues within 4Å: Chain B: 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: 9 residues within 4Å: Chain A: S.704, A.706, S.708, N.710, S.711, E.1072, K.1073, N.1074 Chain B: Q.895 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.706, A:S.708, A:S.711 NAG-NAG-FUC.18: 6 residues within 4Å: Chain A: Q.895 Chain C: A.706, A.713, E.1072, K.1073, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.28: 10 residues within 4Å: Chain B: S.704, A.706, S.708, N.710, S.711, A.713, E.1072, K.1073, N.1074 Chain C: Q.895 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.706, B:S.708

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

NAG.31: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.33: 6 residues within 4Å: Chain A: G.339, F.342, N.343, L.368, S.371, F.374 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: Y.655, V.656, N.657 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain A: N.709, N.710, I.1130, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.39: 7 residues within 4Å: Chain B: F.338, G.339, F.342, N.343, V.367, L.368, F.374 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: Y.655, N.657 Ligand excluded by PLIP NAG.42: 6 residues within 4Å: Chain B: N.709, N.710, I.1130, G.1131 Chain C: I.794, D.796 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.45: 6 residues within 4Å: Chain C: G.339, F.342, N.343, L.368, S.371, 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, Y.655, V.656, N.657 Ligand excluded by PLIP NAG.48: 6 residues within 4Å: Chain A: I.794, D.796 Chain C: N.709, N.710, 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
B

C
C

Spike glycoprotein