SMTL ID : 8xmg.1

Cryo-EM structure of SARS-CoV-2 Omicron HV.1 spike protein(6P), RBD-closed state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.104, T.106, N.107, V.109 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: E.114, N.145, N.146 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: N.261, E.262, N.263 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.312, Q.561 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: N.597, T.599, E.600, Q.625 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.698, Q.1052 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.782, S.784, Q.785 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: N.690, I.1111 Chain B: I.775, Y.777 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: A.687, E.1053, N.1055 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.638 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: N.1079, T.1081, H.1082, F.1084 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: I.1113, V.1114, N.1115 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain B: N.104, T.106, N.107, V.109 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: N.145, N.146 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: K.539 Chain B: E.262, N.263 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.312 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: N.597, C.598, T.599, Q.625 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: N.698, L.903, Q.1052 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.782, S.784 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.215, T.217 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.690 Chain C: Y.777 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: A.687, E.1053, N.1055 Chain C: Q.876 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: C.1107, I.1113, N.1115 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: Y.636, N.638 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain B: Y.10, T.11, N.12, S.42, N.43 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: N.1079, T.1081, H.1082, F.1084 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain C: N.104, T.106, N.107, V.109 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: E.262, N.263 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: N.312, P.560, Q.561, L.563 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: N.597, Q.625 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.698, L.903, Q.1052 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.782, S.784, Q.785 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: T.90, N.215 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: Y.777 Chain C: N.690 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: E.1053, N.1055 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.1115 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.324, T.326 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: Y.10, N.43, T.45 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, L. et al., Spike structures, receptor binding, and immune escape of recently circulating SARS-CoV-2 Omicron BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 sub-variants. Structure (2024)

Release Date

2024-07-03

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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