› 7y3n

X-ray diffraction
2.97Å resolution

Crystal structure of SARS-CoV receptor binding domain in complex with human antibody BIOLS56

Released:
DOI: 10.2210/pdb7y3n/pdb
PDB entry 7y3n coloured by chain, front view.
PDB entry 7y3n coloured by chain, side view.
PDB entry 7y3n coloured by chain, top view.
Source organisms:
Primary publication:
Defining a de novo non-RBM antibody as RBD-8 and its synergistic rescue of immune-evaded antibodies to neutralize Omicron SARS-CoV-2.
Rao X, Zhao R, Tong Z, Guo S, Peng W, Liu K, Li S, Wu L, Tong J, Chai Y, Han P, Wang F, Jia P, Li Z, Zhao X, Li D, Zhang R, Zhang X, Zou W, Li W, Wang Q, Gao GF, Wu Y, Dai L, Gao F
OpenAccess logo Proc Natl Acad Sci U S A 120 e2314193120 (2023)
PMID: 38109549

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-548077 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Spike protein S1 Chains: A, B, E
Molecule details ›
Chains: A, B, E
Length: 228 amino acids
Theoretical weight: 25.86 KDa
Source organism: Severe acute respiratory syndrome-related coronavirus
Expression system: Homo sapiens
UniProt:
  • Canonical: P59594 (Residues: 306-527; Coverage: 18%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
Heavy chain of BIOLS56 Chains: C, F, H
Molecule details ›
Chains: C, F, H
Length: 237 amino acids
Theoretical weight: 25.34 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Light chain of BIOLS56 Chains: D, G, L
Molecule details ›
Chains: D, G, L
Length: 215 amino acids
Theoretical weight: 23.43 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 112.483Å b: 159.018Å c: 175.99Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.22 0.263
Expression system: Homo sapiens

Quick links

Citations

2 citation in other articles

Broadening sarbecovirus neutralization with bispecific antibodies combining distinct conserved targets on the receptor binding domain.
Guerra et al. (2024)
1 more