› 7kfv

X-ray diffraction
2.1Å resolution

Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-B12 Fab)

Released:
DOI: 10.2210/pdb7kfv/pdb
PDB entry 7kfv coloured by chain, front view.
PDB entry 7kfv coloured by chain, side view.
PDB entry 7kfv coloured by chain, top view.
Source organisms:
Primary publication:
Molecular basis for a germline-biased neutralizing antibody response to SARS-CoV-2.
Clark SA, Clark LE, Pan J, Coscia A, McKay LGA, Shankar S, Johnson RI, Griffiths A, Abraham J
bioRxiv (2020)
PMID: 33200128

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-209791 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Spike protein S1 Chains: A, B, E
Molecule details ›
Chains: A, B, E
Length: 228 amino acids
Theoretical weight: 25.47 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 319-541; Coverage: 18%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
Heavy chain of antibody C1A-B12 Fab Chains: C, F, H
Molecule details ›
Chains: C, F, H
Length: 225 amino acids
Theoretical weight: 23.82 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
light chain of antibody C1A-B3 Fab Chains: D, G, L
Molecule details ›
Chains: D, G, L
Length: 214 amino acids
Theoretical weight: 23.22 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Ligands and Environments

1 bound ligand:
Ligand NAG 3 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P212121
Unit cell:
a: 84.834Å b: 113.25Å c: 268.878Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.183 0.216
Expression system: Homo sapiens

Quick links

Citations

12 mentions without citation

Structural and antigenic variations in the spike protein of emerging SARS-CoV-2 variants.
Mittal et al. (2022)
11 more