› 8h5u

X-ray diffraction
2.4Å resolution

Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with neutralizing nanobody Nb-021

Released:
DOI: 10.2210/pdb8h5u/pdb
PDB entry 8h5u coloured by chain, front view.
PDB entry 8h5u coloured by chain, side view.
PDB entry 8h5u coloured by chain, top view.
Source organisms:
Primary publication:
Development of a bispecific nanobody conjugate broadly neutralizes diverse SARS-CoV-2 variants and structural basis for its broad neutralization.
Yang J, Lin S, Chen Z, Yang F, Guo L, Wang L, Duan Y, Zhang X, Dai Y, Yin K, Yu C, Yuan X, Sun H, He B, Cao Y, Ye H, Dong H, Liu X, Chen B, Li J, Zhao Q, Lu G
OpenAccess logo PLoS Pathog 19 e1011804 (2023)
PMID: 38033141

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-272920 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Spike protein S1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 218 amino acids
Theoretical weight: 24.5 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P0DTC2 (Residues: 320-537; Coverage: 17%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
Nanobody Nb-021 Chains: B, D
Molecule details ›
Chains: B, D
Length: 119 amino acids
Theoretical weight: 12.86 KDa
Source organism: Vicugna pacos
Expression system: Brevibacillus choshinensis

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
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: 78.072Å b: 104.827Å c: 107.053Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.225 0.245
Expression systems:
  • Spodoptera frugiperda
  • Brevibacillus choshinensis

Quick links

Citations

3 review citations

Nanobodies in the fight against infectious diseases: repurposing nature's tiny weapons.
Rizk et al. (2024)
2 more