SMTL ID : 9cre.1

Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Alpha (B.1.1.7) 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: 5 residues within 4Å: Chain A: N.120, T.122, N.123, V.125, V.168 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: 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: 4 residues within 4Å: Chain A: N.277, E.278, 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: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) 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 No protein-ligand interaction detected (PLIP) 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: 4 residues within 4Å: Chain B: N.277, E.278, N.279 Chain C: K.555 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: N.613, T.615, Q.641 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: 5 residues within 4Å: Chain C: N.120, T.122, N.123, V.125, V.168 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain C: E.130, N.161, N.162 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain C: T.106, N.231 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain A: K.555 Chain C: N.277, E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain C: N.613, T.615, Q.641 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 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: 3 residues within 4Å: Chain A: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) 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:N.1071 NAG-NAG-FUC.28: 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.31: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: F.335, G.336, F.339, N.340 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: N.706, G.1128 Chain C: D.793 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain B: F.335, G.336, F.339, N.340 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain A: D.793 Chain B: N.706, G.1128 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: F.335, G.336, F.339, N.340 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain B: D.793 Chain C: N.706, G.1128 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.37: 3 residues within 4Å: Chain A: H.1115 Chain B: H.1115 Chain C: H.1115 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Metal complexes: C:H.1115, A:H.1115, B:H.1115

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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