› 6yla

X-ray diffraction
2.42Å resolution

Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab

Released:
DOI: 10.2210/pdb6yla/pdb
PDB entry 6yla coloured by chain, front view.
PDB entry 6yla coloured by chain, side view.
PDB entry 6yla coloured by chain, top view.
Source organisms:
Primary publication:
Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike.
Huo J, Zhao Y, Ren J, Zhou D, Duyvesteyn HME, Ginn HM, Carrique L, Malinauskas T, Ruza RR, Shah PNM, Tan TK, Rijal P, Coombes N, Bewley KR, Tree JA, Radecke J, Paterson NG, Supasa P, Mongkolsapaya J, Screaton GR, Carroll M, Townsend A, Fry EE, Owens RJ, Stuart DI
Cell Host Microbe 28 445-454.e6 (2020)
PMID: 32585135

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-209678 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Spike protein S1 Chains: A, E
Molecule details ›
Chains: A, E
Length: 213 amino acids
Theoretical weight: 24 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 330-532; Coverage: 16%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
Heavy Chain Chains: B, H
Molecule details ›
Chains: B, H
Length: 229 amino acids
Theoretical weight: 24.46 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Light chain Chains: C, L
Molecule details ›
Chains: C, L
Length: 220 amino acids
Theoretical weight: 24.29 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Ligands and Environments

5 bound ligands:
Ligand DMS 14 x DMS
Ligand MLI 12 x MLI
Ligand NAG 3 x NAG
Ligand 1PE 2 x 1PE
Ligand PG0 1 x PG0
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P41212
Unit cell:
a: 163.124Å b: 163.124Å c: 189.076Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.213 0.237
Expression system: Homo sapiens

Quick links

Citations

31 review citations

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

57 mentions without citation

Structure of SARS-CoV-2 spike protein.
Zhang et al. (2021)
56 more