› 5ca6

X-ray diffraction
1.9Å resolution

Crystallographic structure of apo porcine rotavirus TFR-41 VP8*

Released:
DOI: 10.2210/pdb5ca6/pdb
PDB entry 5ca6 coloured by chain, front view.
PDB entry 5ca6 coloured by chain, side view.
PDB entry 5ca6 coloured by chain, top view.
Source organism: Porcine rotavirus serotype 5/strain TFR-41
Primary publication:
Substantial Receptor-induced Structural Rearrangement of Rotavirus VP8*: Potential Implications for Cross-Species Infection.
Yu X, Mishra R, Holloway G, von Itzstein M, Coulson BS, Blanchard H
Chembiochem 16 2176-81 (2015)
PMID: 26250751

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-103226 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Outer capsid protein VP4 Chains: A, B
Molecule details ›
Chains: A, B
Length: 161 amino acids
Theoretical weight: 18.15 KDa
Source organism: Porcine rotavirus serotype 5/strain TFR-41
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A1A9TAH8 (Residues: 1-161; Coverage: 100%)
Sequence domains: Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain
Structure domains: Jelly Rolls

Ligands and Environments

4 bound ligands:
Ligand GOL 6 x GOL
Ligand FMT 4 x FMT
Ligand PLM 1 x PLM
Ligand VCA 1 x VCA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: C2
Unit cell:
a: 134.816Å b: 30.444Å c: 86.217Å
α: 90° β: 124.05° γ: 90°
R-values:
R R work R free
0.166 0.164 0.203
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Histo-blood group antigens as mediators of infections.
Heggelund et al. (2017)
2 other articles

1 mention without citation

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