SMTL ID : 9crf.1

Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Alpha (B.1.1.7) 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.120, A.121, T.122, N.123, V.125, V.168 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: E.130, N.161, N.162 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: T.106, N.231 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.277, N.279 Chain B: K.555 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.613, T.615, Q.641 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.714, L.919 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.919 NAG-NAG.7: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain B: N.120, T.122, N.123, V.125, V.168 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.168 Hydrogen bonds: B:N.123 NAG-NAG.12: 3 residues within 4Å: Chain B: E.130, N.161, N.162 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain B: T.106, N.231 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain B: N.277, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain B: N.613, T.615 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 7 residues within 4Å: Chain C: N.120, A.121, T.122, N.123, V.125, E.151, V.168 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain C: T.106, N.231, T.233 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain A: K.555 Chain C: N.277, E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain C: N.613, T.615 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 1 residues within 4Å: Chain C: N.1131 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: 5 residues within 4Å: Chain A: S.701, A.703, S.705, E.1069, N.1071 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.703, A:S.705 NAG-NAG-FUC.18: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.703, B:N.1071 NAG-NAG-FUC.27: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP)

18 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: 5 residues within 4Å: Chain A: R.325, N.328, I.329, Q.577, T.578 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: F.335, G.336, F.339, N.340 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: N.706 Chain C: D.793 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.328 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: G.336, F.339, N.340 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: H.652, N.654 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain A: D.793 Chain B: N.706, G.1128 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: N.328, Q.577, T.578 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: G.336, F.339, N.340 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: H.652, N.654 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain B: D.793 Chain C: N.706, N.707 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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