› 3sit

X-ray diffraction
1.8Å resolution

Crystal structure of porcine CRW-8 Rotavirus VP8* in complex with aceramido-GM3

Released:
DOI: 10.2210/pdb3sit/pdb
PDB entry 3sit coloured by chain, front view.
PDB entry 3sit coloured by chain, side view.
PDB entry 3sit coloured by chain, top view.
Source organism: Porcine rotavirus (serotype 3 / strain CRW-8)
Primary publication:
Novel structural insights into rotavirus recognition of ganglioside glycan receptors.
Yu X, Coulson BS, Fleming FE, Dyason JC, von Itzstein M, Blanchard H
J Mol Biol 413 929-39 (2011)
PMID: 21945555

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-143143 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Outer capsid protein VP8* Chains: A, B
Molecule details ›
Chains: A, B
Length: 163 amino acids
Theoretical weight: 18.46 KDa
Source organism: Porcine rotavirus (serotype 3 / strain CRW-8)
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0C6Y8 (Residues: 64-224; Coverage: 21%)
Sequence domains: Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain
Structure domains: Jelly Rolls

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, GAL, SIA
Carbohydrate polymer
2 bound ligands:
Ligand NA 2 x NA
Ligand MRD 2 x MRD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P212121
Unit cell:
a: 56.777Å b: 57.357Å c: 113.129Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.184 0.213
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

8 review citations

Diversity in Rotavirus-Host Glycan Interactions: A "Sweet" Spectrum.
Ramani et al. (2016)
7 more

1 mention without citation

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