› 5vki

X-ray diffraction
1.9Å resolution

Crystal structure of P[19] rotavirus VP8* complexed with mucin core 2

Released:
DOI: 10.2210/pdb5vki/pdb
PDB entry 5vki coloured by chain, front view.
PDB entry 5vki coloured by chain, side view.
PDB entry 5vki coloured by chain, top view.
Source organism: Human rotavirus A
Primary publication:
Structural basis of glycan specificity of P[19] VP8*: Implications for rotavirus zoonosis and evolution.
Liu Y, Xu S, Woodruff AL, Xia M, Tan M, Kennedy MA, Jiang X
OpenAccess logo PLoS Pathog 13 e1006707 (2017)
PMID: 29136651

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-108507 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Outer capsid protein VP8* Chains: A, B
Molecule details ›
Chains: A, B
Length: 160 amino acids
Theoretical weight: 18.17 KDa
Source organism: Human rotavirus A
Expression system: Escherichia coli
UniProt:
  • Canonical: A7YCM0 (Residues: 64-223; Coverage: 21%)
Gene name: VP4
Sequence domains: Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain
Structure domains: Jelly Rolls

Ligands and Environments

Carbohydrate polymer : NEW Components: NGA, GAL, NAG
Carbohydrate polymer
3 bound ligands:
Ligand SO4 2 x SO4
Ligand GOL 2 x GOL
Ligand THR 2 x THR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: I41
Unit cell:
a: 115.861Å b: 115.861Å c: 101.76Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.221 0.24
Expression system: Escherichia coli

Quick links

Citations

8 review citations

The Impact of Human Genetic Polymorphisms on Rotavirus Susceptibility, Epidemiology, and Vaccine Take.
Sharma et al. (2020)
7 more

3 mentions without citation

Structural Basis of Glycan Recognition of Rotavirus.
Sun et al. (2021)
2 more