SMTL ID : 8y5j.1

Cryo-EM structure of SARS-CoV-2 Omicron JN.1 spike protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 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: 3 residues within 4Å: Chain A: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP)

1 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.4: 4 residues within 4Å: Chain C: N.351, R.352, T.353, R.354 No protein-ligand interaction detected (PLIP)

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

NAG.5: 2 residues within 4Å: Chain A: N.612, T.614 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.705 Chain B: Y.792 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.713, Q.922, Q.1067 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: N.1070, F.1071, T.1072, S.1093 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: N.1094, T.1096, H.1097, F.1099 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.1130 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: T.107, T.113, N.231 Chain C: E.462 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: E.278, N.279 Chain C: K.554 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: P.327, N.328, P.575, Q.576 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.351, R.352, T.353 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: N.612, T.614 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.705 Chain C: K.791, Y.792 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.713, Q.1067 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.1070 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: N.1094, T.1096, H.1097, F.1099 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.1130 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.328, V.329, Q.576 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: N.612, T.614 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: Y.792 Chain C: N.705 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: N.713, Q.922, Q.1067 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: Q.891 Chain C: N.1070 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain C: N.1094, T.1096, H.1097, F.1099 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.1130 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: N.328, P.575, Q.576 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: K.554 Chain C: N.277, N.279 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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