› 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 5kov coloured by chain and viewed from the front.
PDB 5kov coloured by chain and viewed from the side.
PDB 5kov coloured by chain and viewed from the top.
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. (2016)
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)
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

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Citations

6 review citations

Structural Insights into the Human Astrovirus Capsid.
Ykema et al. (2021)
5 more

3 mentions without citation

Structure of a Human Astrovirus Capsid-Antibody Complex and Mechanistic Insights into Virus Neutralization.
Bogdanoff et al. (2017)
2 more