› 4opo

X-ray diffraction
1.4Å resolution

Crystal structure of P domain from norovirus strain Saga4 in complex with HBGA type Leb (tetraglycan)

Released:
DOI: 10.2210/pdb4opo/pdb
PDB entry 4opo coloured by chain, front view.
PDB entry 4opo coloured by chain, side view.
PDB entry 4opo coloured by chain, top view.
Source organism: Norovirus Hu/GII-4/Kumamoto5/2006/JP
Primary publication:
Human noroviruses' fondness for histo-blood group antigens.
Singh BK, Leuthold MM, Hansman GS
J Virol 89 2024-40 (2015)
PMID: 25428879

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110183 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
VP1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 309 amino acids
Theoretical weight: 34.04 KDa
Source organism: Norovirus Hu/GII-4/Kumamoto5/2006/JP
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B5BTT5 (Residues: 225-530; Coverage: 57%)
Sequence domains: Calicivirus coat protein C-terminal
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, GAL, FUC
Carbohydrate polymer
2 bound ligands:
Ligand ACT 2 x ACT
Ligand EDO 5 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: C2
Unit cell:
a: 113.66Å b: 58.6Å c: 97.17Å
α: 90° β: 107.15° γ: 90°
R-values:
R R work R free
0.152 0.151 0.185
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

15 review citations

Human Milk Oligosaccharides as Promising Antivirals.
Morozov et al. (2018)
14 more

3 mentions without citation

Human noroviruses' fondness for histo-blood group antigens.
Singh et al. (2015)
2 more