› 3sej

X-ray diffraction
3.04Å resolution

Structural characterization of a GII.4 2004 norovirus variant (TCH05) bound to Secretor Lewis HBGA (LeB)

Released:
DOI: 10.2210/pdb3sej/pdb
PDB entry 3sej coloured by chain, front view.
PDB entry 3sej coloured by chain, side view.
PDB entry 3sej coloured by chain, top view.
Source organism: Norovirus Hu/GII.4/2004/NL
Primary publication:
Structural analysis of histo-blood group antigen binding specificity in a norovirus GII.4 epidemic variant: implications for epochal evolution.
Shanker S, Choi JM, Sankaran B, Atmar RL, Estes MK, Prasad BV
J Virol 85 8635-45 (2011)
PMID: 21715503

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-177022 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Capsid Chains: A, B, C, D, E, F, G, H, I, J
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J
Length: 311 amino acids
Theoretical weight: 34.33 KDa
Source organism: Norovirus Hu/GII.4/2004/NL
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5EGK8 (Residues: 221-531; Coverage: 58%)
Sequence domains: Calicivirus coat protein C-terminal
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: BGC, GAL, NAG, FUC
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: C2221
Unit cell:
a: 242.74Å b: 339.779Å c: 125.021Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.169 0.166 0.223
Expression system: Escherichia coli

Quick links

Citations

19 review citations

Norovirus.
Robilotti et al. (2015)
18 more

4 mentions without citation

Structural analysis of histo-blood group antigen binding specificity in a norovirus GII.4 epidemic variant: implications for epochal evolution.
Shanker et al. (2011)
3 more