› 6xc4

X-ray diffraction
2.34Å resolution

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC12.3

Released:
DOI: 10.2210/pdb6xc4/pdb
PDB entry 6xc4 coloured by chain, front view.
PDB entry 6xc4 coloured by chain, side view.
PDB entry 6xc4 coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of a shared antibody response to SARS-CoV-2.
Yuan M, Liu H, Wu NC, Lee CD, Zhu X, Zhao F, Huang D, Yu W, Hua Y, Tien H, Rogers TF, Landais E, Sok D, Jardine JG, Burton DR, Wilson IA
Science 369 1119-1123 (2020)
PMID: 32661058

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-209672 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Spike protein S1 Chains: A, Z
Molecule details ›
Chains: A, Z
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
CC12.3 heavy chain Chains: H, X
Molecule details ›
Chains: H, X
Length: 220 amino acids
Theoretical weight: 23.38 KDa
Source organism: Homo sapiens
Expression system: Mus musculus
CC12.3 light chain Chains: L, Y
Molecule details ›
Chains: L, Y
Length: 215 amino acids
Theoretical weight: 23.43 KDa
Source organism: Homo sapiens
Expression system: Mus musculus

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-1
Spacegroup: P21
Unit cell:
a: 56.071Å b: 105.59Å c: 165.937Å
α: 90° β: 92.77° γ: 90°
R-values:
R R work R free
0.186 0.184 0.219
Expression systems:
  • Trichoplusia ni
  • Mus musculus

Quick links

Citations

43 review citations

Structural biology of SARS-CoV-2 and implications for therapeutic development.
Yang et al. (2021)
42 more

46 mentions without citation

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