› 7jmp

X-ray diffraction
1.71Å resolution

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-39

Released:
DOI: 10.2210/pdb7jmp/pdb
PDB entry 7jmp coloured by chain, front view.
PDB entry 7jmp coloured by chain, side view.
PDB entry 7jmp coloured by chain, top view.
Source organisms:
Primary publication:
An Alternative Binding Mode of IGHV3-53 Antibodies to the SARS-CoV-2 Receptor Binding Domain.
Wu NC, Yuan M, Liu H, Lee CD, Zhu X, Bangaru S, Torres JL, Caniels TG, Brouwer PJM, van Gils MJ, Sanders RW, Ward AB, Wilson IA
OpenAccess logo Cell Rep 33 108274 (2020)
PMID: 33027617

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-276076 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Spike protein S1 Chain: A
Molecule details ›
Chain: A
Length: 231 amino acids
Theoretical weight: 26.1 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P0DTC2 (Residues: 319-541; Coverage: 18%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
COVA2-39 heavy chain Chain: H
Molecule details ›
Chain: H
Length: 232 amino acids
Theoretical weight: 24.71 KDa
Source organism: Homo sapiens
Expression system: Mus musculus
COVA2-39 light chain Chain: L
Molecule details ›
Chain: L
Length: 216 amino acids
Theoretical weight: 22.75 KDa
Source organism: Homo sapiens
Expression system: Mus musculus

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-1
Spacegroup: P21
Unit cell:
a: 68.905Å b: 80.445Å c: 72.006Å
α: 90° β: 104.88° γ: 90°
R-values:
R R work R free
0.178 0.177 0.209
Expression systems:
  • Trichoplusia ni
  • Mus musculus

Quick links

Citations

19 review citations

SARS-CoV-2 Vaccines Based on the Spike Glycoprotein and Implications of New Viral Variants.
Martínez-Flores et al. (2021)
18 more

43 mentions without citation

Recognition of the SARS-CoV-2 receptor binding domain by neutralizing antibodies.
Yuan et al. (2021)
42 more