7fh0

X-ray diffraction
3.2Å resolution

Crystallographic structure of two neutralizing nanobodies in complex with SARS-CoV-2 spike receptor-binding Domain (RBD)

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-225177 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Spike protein S1 Chain: A
Molecule details ›
Chain: A
Length: 438 amino acids
Theoretical weight: 49.3 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P0DTC2 (Residues: 309-537; Coverage: 18%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
nanobodies aRBD-2-7 Chains: B, C
Molecule details ›
Chains: B, C
Length: 261 amino acids
Theoretical weight: 28.13 KDa
Source organism: Vicugna pacos
Expression system: Komagataella pastoris

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P6522
Unit cell:
a: 154.456Å b: 154.456Å c: 257.916Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.21 0.208 0.263
Expression systems:
  • Cricetulus griseus
  • Komagataella pastoris