› 7u2d

X-ray diffraction
2.76Å resolution

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody ADG20

Released:
DOI: 10.2210/pdb7u2d/pdb
PDB entry 7u2d coloured by chain, front view.
PDB entry 7u2d coloured by chain, side view.
PDB entry 7u2d coloured by chain, top view.
Source organisms:
Primary publication:
A broad and potent neutralization epitope in SARS-related coronaviruses.
Yuan M, Zhu X, He WT, Zhou P, Kaku CI, Capozzola T, Zhu CY, Yu X, Liu H, Yu W, Hua Y, Tien H, Peng L, Song G, Cottrell CA, Schief WR, Nemazee D, Walker LM, Andrabi R, Burton DR, Wilson IA
Proc Natl Acad Sci U S A 119 e2205784119 (2022)
PMID: 35767670

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-233244 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Spike protein S1 Chain: A
Molecule details ›
Chain: A
Length: 205 amino acids
Theoretical weight: 23.1 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P0DTC2 (Residues: 333-530; Coverage: 16%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
ADG20 heavy chain Chain: H
Molecule details ›
Chain: H
Length: 227 amino acids
Theoretical weight: 24.13 KDa
Source organism: Homo sapiens
Expression system: Mus musculus
ADG20 light chain Chain: L
Molecule details ›
Chain: L
Length: 218 amino acids
Theoretical weight: 22.95 KDa
Source organism: Homo sapiens
Expression system: Mus musculus

Ligands and Environments

3 bound ligands:
Ligand NAG 1 x NAG
Ligand SO4 5 x SO4
Ligand CIT 1 x CIT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P41
Unit cell:
a: 101.083Å b: 101.083Å c: 80.607Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.22 0.259
Expression systems:
  • Trichoplusia ni
  • Mus musculus

Quick links

Citations

7 review citations

Monoclonal antibody therapies against SARS-CoV-2.
Focosi et al. (2022)
6 more

4 mentions without citation

A broad and potent neutralization epitope in SARS-related coronaviruses.
Yuan et al. (2022)
3 more