› 8zc5

Electron Microscopy
3.91Å resolution

SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with D1F6 Fab, focused refinement of RBD region

Released:
DOI: 10.2210/pdb8zc5/pdb
PDB entry 8zc5 coloured by chain, front view.
PDB entry 8zc5 coloured by chain, side view.
PDB entry 8zc5 coloured by chain, top view.
Source organisms:
Primary publication:
An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike.
Liu B, Niu X, Deng Y, Zhang Z, Wang Y, Gao X, Liang H, Li Z, Wang Q, Cheng Y, Chen Q, Huang S, Pan Y, Su M, Lin X, Niu C, Chen Y, Yang W, Zhang Y, Yan Q, He J, Zhao J, Chen L, Xiong X
Cell Rep 43 114265 (2024)
PMID: 38805396
Related structures: EMD-39923

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-535246 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Spike protein S1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 196 amino acids
Theoretical weight: 22.12 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 332-527; Coverage: 16%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
Light chain of D1F6 Fab Chains: C, D
Molecule details ›
Chains: C, D
Length: 110 amino acids
Theoretical weight: 11.62 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Heavy chain of D1F6 Fab Chains: E, F
Molecule details ›
Chains: E, F
Length: 127 amino acids
Theoretical weight: 14.18 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Ligands and Environments

1 bound ligand:
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.91Å
Relevant EMDB volumes: EMD-39923
Expression system: Homo sapiens

Quick links

Citations

1 citations in other articles

Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein and potentially drive the genesis of Omicron variants.
Yan et al. (2024)