› 7rku

X-ray diffraction
3.2Å resolution

Structure of the SARS-CoV-2 receptor binding domain in complex with the human neutralizing antibody Fab fragment, C022

Released:
DOI: 10.2210/pdb7rku/pdb
PDB entry 7rku coloured by chain, front view.
PDB entry 7rku coloured by chain, side view.
PDB entry 7rku coloured by chain, top view.
Source organisms:
Primary publication:
Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies.
Jette CA, Cohen AA, Gnanapragasam PNP, Muecksch F, Lee YE, Huey-Tubman KE, Schmidt F, Hatziioannou T, Bieniasz PD, Nussenzweig MC, West AP, Keeffe JR, Bjorkman PJ, Barnes CO
OpenAccess logo Cell Rep 36 109760 (2021)
PMID: 34534459

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-209905 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Spike protein S1 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 212 amino acids
Theoretical weight: 24 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 328-533; Coverage: 16%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
C022 Antibody Fab Heavy Chain Chains: E, G, H, J
Molecule details ›
Chains: E, G, H, J
Length: 240 amino acids
Theoretical weight: 25.98 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
C022 Antibody Fab Light Chain Chains: F, I, K, L
Molecule details ›
Chains: F, I, K, L
Length: 215 amino acids
Theoretical weight: 23.61 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
1 bound ligand:
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P61
Unit cell:
a: 178.385Å b: 178.385Å c: 247.318Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.19 0.188 0.231
Expression system: Homo sapiens

Quick links

Citations

8 review citations

Broadly-Neutralizing Antibodies Against Emerging SARS-CoV-2 Variants.
Shrestha et al. (2021)
7 more

8 mentions without citation

How Antibodies Recognize Pathogenic Viruses: Structural Correlates of Antibody Neutralization of HIV-1, SARS-CoV-2, and Zika.
Abernathy et al. (2021)
7 more