› 7cyv

X-ray diffraction
3.13Å resolution

Crystal structure of FD20, a neutralizing single-chain variable fragment (scFv) in complex with SARS-CoV-2 Spike receptor-binding domain (RBD)

Released:
DOI: 10.2210/pdb7cyv/pdb
PDB entry 7cyv coloured by chain, front view.
PDB entry 7cyv coloured by chain, side view.
PDB entry 7cyv coloured by chain, top view.
Source organisms:
Primary publication:
Uncovering a conserved vulnerability site in SARS-CoV-2 by a human antibody.
Li T, Cai H, Zhao Y, Li Y, Lai Y, Yao H, Liu LD, Sun Z, van Vlissingen MF, Kuiken T, GeurtsvanKessel CH, Zhang N, Zhou B, Lu L, Gong Y, Qin W, Mondal M, Duan B, Xu S, Richard AS, Raoul H, Chen J, Xu C, Wu L, Zhou H, Huang Z, Zhang X, Li J, Wang Y, Bi Y, Rockx B, Chen J, Meng FL, Lavillette D, Li D
OpenAccess logo EMBO Mol Med 13 e14544 (2021)
PMID: 34672091

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-534753 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
The heavy chain variable region of the scFv FD20,The light chain variable region of the scFv FD20 Chain: H
Molecule details ›
Chain: H
Length: 281 amino acids
Theoretical weight: 29.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
Spike protein S1 Chain: B
Molecule details ›
Chain: B
Length: 213 amino acids
Theoretical weight: 23.83 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

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, FUC
Carbohydrate polymer
No bound ligands
1 modified residue:
Ligand TPO 1 x TPO

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: C2
Unit cell:
a: 206.958Å b: 57.925Å c: 47.207Å
α: 90° β: 100.433° γ: 90°
R-values:
R R work R free
0.253 0.252 0.276
Expression systems:
  • Escherichia coli BL21(DE3)
  • Trichoplusia ni

Quick links

Citations

1 review citation

Comprehensive Overview of Broadly Neutralizing Antibodies against SARS-CoV-2 Variants.
Cui et al. (2024)
11 other articles

4 mentions without citation

Uncovering a conserved vulnerability site in SARS-CoV-2 by a human antibody.
Li et al. (2021)
3 more