› 5kov

X-ray diffraction
3.24Å resolution

Crystal structure of the human astrovirus 2 capsid protein spike in complex with a single chain variable fragment of an astrovirus neutralizing antibody at 3.24-A resolution

Released:
DOI: 10.2210/pdb5kov/pdb
PDB entry 5kov coloured by chain, front view.
PDB entry 5kov coloured by chain, side view.
PDB entry 5kov coloured by chain, top view.
Source organisms:
Primary publication:
Structure of a Human Astrovirus Capsid-Antibody Complex and Mechanistic Insights into Virus Neutralization.
Bogdanoff WA, Campos J, Perez EI, Yin L, Alexander DL, DuBois RM
J Virol 91 (2017)
PMID: 27807234

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-231399 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Capsid protein VP25 Chains: A, B, G, H, M, N, S, T
Molecule details ›
Chains: A, B, G, H, M, N, S, T
Length: 228 amino acids
Theoretical weight: 25.98 KDa
Source organism: Human astrovirus 2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q82446 (Residues: 429-644; Coverage: 27%)
Gene name: ORF2
Sequence domains: Turkey astrovirus capsid protein
PL-2 scFv chain Chains: C, E, I, K, O, Q, U, W
Molecule details ›
Chains: C, E, I, K, O, Q, U, W
Length: 251 amino acids
Theoretical weight: 26.73 KDa
Source organism: Mus musculus
Expression system: Drosophila melanogaster
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand NAG 4 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P41
Unit cell:
a: 199.998Å b: 199.998Å c: 157.515Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.243 0.241 0.288
Expression systems:
  • Escherichia coli BL21(DE3)
  • Drosophila melanogaster

Quick links

Citations

6 review citations

Astrovirus Biology and Pathogenesis.
Cortez et al. (2017)
5 more

3 mentions without citation

An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants.
Guest et al. (2021)
2 more