› 3asp

X-ray diffraction
1.6Å resolution

Crystal structure of P domain from Norovirus Funabashi258 stain in the complex with A-antigen

Released:
DOI: 10.2210/pdb3asp/pdb
PDB entry 3asp coloured by chain, front view.
PDB entry 3asp coloured by chain, side view.
PDB entry 3asp coloured by chain, top view.
Source organism: Norwalk-like virus
Primary publication:
Structural basis for the recognition of Lewis antigens by genogroup I norovirus.
Kubota T, Kumagai A, Ito H, Furukawa S, Someya Y, Takeda N, Ishii K, Wakita T, Narimatsu H, Shirato H
J Virol 86 11138-50 (2012)
PMID: 22855491

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185040 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Capsid protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 326 amino acids
Theoretical weight: 35.26 KDa
Source organism: Norwalk-like virus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8JW44 (Residues: 221-541; Coverage: 59%)
Gene name: capsid
Sequence domains: Calicivirus coat protein C-terminal
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, GAL, FUC, A2G
Carbohydrate polymer
1 bound ligand:
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P31
Unit cell:
a: 74.624Å b: 74.624Å c: 106.996Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.183 0.182 0.201
Expression system: Escherichia coli

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Citations

9 review citations

Histo-blood group antigens: a common niche for norovirus and rotavirus.
Tan et al. (2014)
8 more

9 mentions without citation

Viruses in Rodent Colonies: Lessons Learned from Murine Noroviruses.
Karst et al. (2015)
8 more