› 7wrl

Electron Microscopy
3.51Å resolution

Local structure of BD55-1239 Fab and SARS-COV2 Omicron RBD complex

Released:
DOI: 10.2210/pdb7wrl/pdb
PDB entry 7wrl coloured by chain, front view.
PDB entry 7wrl coloured by chain, side view.
PDB entry 7wrl coloured by chain, top view.
Source organism: SARS coronavirus B012
Primary publication:
BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection.
Cao Y, Yisimayi A, Jian F, Song W, Xiao T, Wang L, Du S, Wang J, Li Q, Chen X, Yu Y, Wang P, Zhang Z, Liu P, An R, Hao X, Wang Y, Wang J, Feng R, Sun H, Zhao L, Zhang W, Zhao D, Zheng J, Yu L, Li C, Zhang N, Wang R, Niu X, Yang S, Song X, Chai Y, Hu Y, Shi Y, Zheng L, Li Z, Gu Q, Shao F, Huang W, Jin R, Shen Z, Wang Y, Wang X, Xiao J, Xie XS
OpenAccess logo Nature (2022)
PMID: 35714668
Related structures: EMD-32732

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-225230 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
BD55-1239H Chain: A
Molecule details ›
Chain: A
Length: 127 amino acids
Theoretical weight: 13.83 KDa
Source organism: SARS coronavirus B012
Expression system: Homo sapiens
BD55-1239L Chain: B
Molecule details ›
Chain: B
Length: 105 amino acids
Theoretical weight: 11.05 KDa
Source organism: SARS coronavirus B012
Expression system: Homo sapiens
Spike protein S1 Chain: R
Molecule details ›
Chain: R
Length: 193 amino acids
Theoretical weight: 21.97 KDa
Source organism: SARS coronavirus B012
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 334-526; Coverage: 15%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.51Å
Relevant EMDB volumes: EMD-32732
Expression system: Homo sapiens

Quick links

Citations

78 review citations

Evolution of the SARS-CoV-2 omicron variants BA.1 to BA.5: Implications for immune escape and transmission.
Shrestha et al. (2022)
77 more

2 mentions without citation

Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.
Huang et al. (2023)
1 more