› 1kqr

X-ray diffraction
1.4Å resolution

Crystal Structure of the Rhesus Rotavirus VP4 Sialic Acid Binding Domain in Complex with 2-O-methyl-alpha-D-N-acetyl neuraminic acid

Released:
DOI: 10.2210/pdb1kqr/pdb
PDB entry 1kqr coloured by chain, front view.
PDB entry 1kqr coloured by chain, side view.
PDB entry 1kqr coloured by chain, top view.
Source organism: Simian rotavirus A strain RRV
Primary publication:
The rhesus rotavirus VP4 sialic acid binding domain has a galectin fold with a novel carbohydrate binding site.
Dormitzer PR, Sun ZY, Wagner G, Harrison SC
EMBO J 21 885-97 (2002)
PMID: 11867517

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146167 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Outer capsid protein VP8* Chain: A
Molecule details ›
Chain: A
Length: 179 amino acids
Theoretical weight: 20.22 KDa
Source organism: Simian rotavirus A strain RRV
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P12473 (Residues: 62-224; Coverage: 21%)
Sequence domains: Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain
Structure domains: Jelly Rolls

Ligands and Environments

3 bound ligands:
Ligand SO4 1 x SO4
Ligand MNA 1 x MNA
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: P41212
Unit cell:
a: 48.027Å b: 48.027Å c: 130.404Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.169 0.169 0.181
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

35 review citations

What does structure tell us about virus evolution?
Bamford et al. (2005)
34 more

42 mentions without citation

The sweet spot: defining virus-sialic acid interactions.
Stencel-Baerenwald et al. (2014)
41 more