› 8y6a

Electron Microscopy
2.72Å resolution

Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 RBD in complex with human ACE2 and S309 Fab

Released:
DOI: 10.2210/pdb8y6a/pdb
PDB entry 8y6a coloured by chain, front view.
PDB entry 8y6a coloured by chain, side view.
PDB entry 8y6a 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-38983

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 tetramer (preferred)
PDBe Complex ID:
PDB-CPX-279636 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (7 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 protein S1 Chain: B
Molecule details ›
Chain: B
Length: 228 amino acids
Theoretical weight: 26.12 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 319-541; Coverage: 18%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
heavy chain of S309 Fab Chain: C
Molecule details ›
Chain: C
Length: 230 amino acids
Theoretical weight: 24.57 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
light chain of S309 Fab Chain: D
Molecule details ›
Chain: D
Length: 214 amino acids
Theoretical weight: 23.2 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand NAG 3 x NAG
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.72Å
Relevant EMDB volumes: EMD-38983
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)