› 7urq

X-ray diffraction
2.05Å resolution

Crystal Structure of SARS-CoV-2 S delta variant receptor-binding domain (RBD) in complex CoV11 Fab crystal form 1

Released:
DOI: 10.2210/pdb7urq/pdb
PDB entry 7urq coloured by chain, front view.
PDB entry 7urq coloured by chain, side view.
PDB entry 7urq coloured by chain, top view.
Source organisms:
Primary publication:
The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11.
Tolbert WD, Chen Y, Sun L, Benlarbi M, Ding S, Manickam R, Pangaro E, Nguyen DN, Gottumukkala S, Côté M, Gonzalez FJ, Finzi A, Tehrani ZR, Sajadi MM, Pazgier M
Front Immunol 14 1178355 (2023)
PMID: 37334379

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-209954 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Spike protein S1 Chain: A
Molecule details ›
Chain: A
Length: 229 amino acids
Theoretical weight: 25.95 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 319-537; Coverage: 17%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
COV11 Fab HEAVY CHAIN Chain: H
Molecule details ›
Chain: H
Length: 221 amino acids
Theoretical weight: 23.36 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
COV11 Fab LIGHT CHAIN Chain: L
Molecule details ›
Chain: L
Length: 216 amino acids
Theoretical weight: 23.54 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Ligands and Environments

2 bound ligands:
Ligand NAG 1 x NAG
Ligand CIT 1 x CIT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Unit cell:
a: 85.818Å b: 103.551Å c: 112.104Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.177 0.208
Expression system: Homo sapiens

Quick links

Citations

1 citations in other articles

Breakthrough infection elicits hypermutated IGHV3-53/3-66 public antibodies with broad and potent neutralizing activity against SARS-CoV-2 variants including the emerging EG.5 lineages.
Li et al. (2023)

1 mention without citation

SARS-CoV-2 Exposure in Norway Rats (Rattus norvegicus) from New York City.
Wang et al. (2023)