SMTL ID : 9crd.1

Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: B.1 variant 1 open RBD

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: 6 residues within 4Å: Chain A: N.122, T.124, N.125, V.126, V.127, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: E.281, N.282 Chain B: K.558 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: N.717, L.922, N.925, Q.926, Q.1071 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.922, A:N.925, A:Q.926 Hydrogen bonds: A:N.925 NAG-NAG.6: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, V.127, V.171 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.171 Hydrogen bonds: B:N.125 NAG-NAG.11: 3 residues within 4Å: Chain B: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: T.108, N.234, T.236 Chain C: E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: N.280, E.281, N.282 Chain C: K.558 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.16: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 6 residues within 4Å: Chain C: N.122, A.123, T.124, N.125, V.127, V.171 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.171 NAG-NAG.21: 3 residues within 4Å: Chain C: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain A: K.558 Chain C: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain C: N.616, T.618 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain C: N.717, L.922, N.925, Q.926, Q.1071 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:N.925, C:Q.926 Hydrogen bonds: C:N.925 NAG-NAG.26: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 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.7: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1074 NAG-NAG-FUC.17: 4 residues within 4Å: Chain B: S.704, A.706, E.1072, N.1074 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1074 NAG-NAG-FUC.27: 4 residues within 4Å: Chain C: A.706, S.711, E.1072, N.1074 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1074

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

NAG.30: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: N.616, T.618 Chain C: I.850 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: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 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: H.655, N.657 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain A: D.796 Chain B: N.709, G.1131 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: 4 residues within 4Å: Chain C: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain B: D.796 Chain C: N.709, 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

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