SMTL ID : 7eb0.1

Cryo-EM structure of SARS-CoV-2 Spike D614G variant, one RBD-up conformation 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 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.1: 2 residues within 4Å: Chain A: T.108, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 3 residues within 4Å: Chain A: E.281, N.282 Chain C: K.558 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 4 residues within 4Å: Chain C: T.108, N.234, I.235, T.236 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.108, C:T.108

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

NAG-NAG.3: 3 residues within 4Å: Chain A: N.331, Q.580, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: F.338, G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.616, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.709, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: S.704, A.706, N.1074 Chain B: Q.895 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.706 NAG-NAG.10: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain B: N.280, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: N.343, S.371, S.373 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.371 NAG-NAG.14: 1 residues within 4Å: Chain B: N.616 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: S.708, N.709, N.710 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain B: N.717, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain B: S.704, V.705, A.706, K.1073, N.1074 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.704, B:A.706 NAG-NAG.19: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain C: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain C: N.616, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain C: S.708, N.709, N.710 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain C: N.717, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain C: S.704, A.706, E.1072, N.1074 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)

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: 1 residues within 4Å: Chain A: N.122 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: H.655, V.656, N.657 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain B: N.122, N.125, V.126, V.127 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: G.232, I.233, N.234 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: E.654, H.655, N.657 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain C: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: N.122, T.124, N.125 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: G.339, F.342, N.343 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, T.J. et al., D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. J.Biol.Chem. (2021)

Release Date

2021-06-23

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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