8hc6

Electron Microscopy
4.69Å resolution

SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with YB9-258 Fab, focused refinement of Fab region

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-225159 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Spike protein S1 Chain: C
Molecule details ›
Chain: C
Length: 267 amino acids
Theoretical weight: 30.24 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 322-588; Coverage: 21%)
Gene names: 2, S
Sequence domains:
Heavy chain of YB9-258 Fab Chain: H
Molecule details ›
Chain: H
Length: 220 amino acids
Theoretical weight: 23.13 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Light chain of YB9-258 Chain: L
Molecule details ›
Chain: L
Length: 215 amino acids
Theoretical weight: 23.18 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Spike protein S1 Chain: B
Molecule details ›
Chain: B
Length: 273 amino acids
Theoretical weight: 31.14 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 14-210, 211-211, 215-289; Coverage: 21%)
Gene names: 2, S
Sequence domains: Betacoronavirus-like spike glycoprotein S1, N-terminal

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.69Å
Relevant EMDB volumes: EMD-34653
Expression system: Homo sapiens