› 7wqv

X-ray diffraction
2.8Å resolution

Crystal structure of a neutralizing monoclonal antibody (Ab08) in complex with SARS-CoV-2 receptor-binding domain (RBD)

Released:
DOI: 10.2210/pdb7wqv/pdb
PDB entry 7wqv coloured by chain, front view.
PDB entry 7wqv coloured by chain, side view.
PDB entry 7wqv coloured by chain, top view.
Source organisms:
Primary publication:
A Spike-destructing human antibody effectively neutralizes Omicron-included SARS-CoV-2 variants with therapeutic efficacy.
Meng L, Zha J, Zhou B, Cao L, Jiang C, Zhu Y, Li T, Lu L, Zhang J, Yang H, Feng J, Gu Z, Tang H, Jiang L, Li D, Lavillette D, Zhang X
OpenAccess logo PLoS Pathog 19 e1011085 (2023)
PMID: 36706160

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-534981 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
Spike protein S1 Chains: A, C, E, G, I, K, M, O
Molecule details ›
Chains: A, C, E, G, I, K, M, O
Length: 234 amino acids
Theoretical weight: 26.21 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P0DTC2 (Residues: 330-531; Coverage: 16%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
Ab08 Chains: B, D, F, H, J, L, N, P
Molecule details ›
Chains: B, D, F, H, J, L, N, P
Length: 303 amino acids
Theoretical weight: 31.37 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli MC1061

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
4 bound ligands:
Ligand MPD 11 x MPD
Ligand CA 6 x CA
Ligand CL 2 x CL
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P21
Unit cell:
a: 92.643Å b: 116.742Å c: 180.72Å
α: 90° β: 90.307° γ: 90°
R-values:
R R work R free
0.221 0.22 0.251
Expression systems:
  • Trichoplusia ni
  • Escherichia coli MC1061

Quick links

Citations

1 review citation

Is there any revival of the use of plasma therapy or neutralizing convalescent antibody therapy to treat SARS-CoV-2 variants and are we rethinking preparedness plans?
Garraud et al. (2023)
4 other articles