› 8y18

Electron Microscopy
3.04Å resolution

Cryo-EM structure of SARS-CoV-2 Omicron JN.1 RBD in complex with human ACE2 (local refinement from the spike protein)

Released:
DOI: 10.2210/pdb8y18/pdb
PDB entry 8y18 coloured by chain, front view.
PDB entry 8y18 coloured by chain, side view.
PDB entry 8y18 coloured by chain, top view.
Source organisms:
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-38827

Function and Biology Details

Reaction catalysed: 
Angiotensin II + H(2)O = angiotensin-(1-7) + L-phenylalanine
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-144194 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
Processed angiotensin-converting enzyme 2 Chain: A
Molecule details ›
Chain: A
Length: 603 amino acids
Theoretical weight: 69.98 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9BYF1 (Residues: 19-615; Coverage: 76%)
Gene names: ACE2, UNQ868/PRO1885
Sequence domains: Angiotensin-converting enzyme
Spike glycoprotein Chain: B
Molecule details ›
Chain: B
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, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand ZN 1 x ZN
Ligand NAG 3 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.04Å
Relevant EMDB volumes: EMD-38827
Expression system: Homo sapiens

Quick links

Citations

1 mention without citation

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)