› 8y5j

Electron Microscopy
2.94Å resolution

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

Released:
DOI: 10.2210/pdb8y5j/pdb
PDB entry 8y5j coloured by chain, front view.
PDB entry 8y5j coloured by chain, side view.
PDB entry 8y5j coloured by chain, top view.
Source organism: Severe acute respiratory syndrome coronavirus 2
Primary publication:
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.
Li L, Shi K, Gu Y, Xu Z, Shu C, Li D, Sun J, Cong M, Li X, Zhao X, Yu G, Hu S, Tan H, Qi J, Ma X, Liu K, Gao GF
Structure (2024)
PMID: 39013463
Related structures: EMD-38937

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-144650 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Spike glycoprotein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 1248 amino acids
Theoretical weight: 138.7 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 1-16, 17-1208; Coverage: 94%)
Gene names: 2, S
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
1 bound ligand:
Ligand NAG 26 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.94Å
Relevant EMDB volumes: EMD-38937
Expression system: Homo sapiens

Quick links

Citations

1 citations in other articles

AlphaFold2 Modeling and Molecular Dynamics Simulations of the Conformational Ensembles for the SARS-CoV-2 Spike Omicron JN.1, KP.2 and KP.3 Variants: Mutational Profiling of Binding Energetics Reveals Epistatic Drivers of the ACE2 Affinity and Escape Hotspots of Antibody Resistance.
Raisinghani et al. (2024)