› 3q39

X-ray diffraction
1.25Å resolution

Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with HBGA type H2 (diglycan)

Released:
DOI: 10.2210/pdb3q39/pdb
PDB entry 3q39 coloured by chain, front view.
PDB entry 3q39 coloured by chain, side view.
PDB entry 3q39 coloured by chain, top view.
Source organism: Norwalk virus
Primary publication:
Crystal structures of GII.10 and GII.12 norovirus protruding domains in complex with histo-blood group antigens reveal details for a potential site of vulnerability.
Hansman GS, Biertümpfel C, Georgiev I, McLellan JS, Chen L, Zhou T, Katayama K, Kwong PD
J Virol 85 6687-701 (2011)
PMID: 21525337

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-177037 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Capsid protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 319 amino acids
Theoretical weight: 34.8 KDa
Source organism: Norwalk virus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5F4T5 (Residues: 224-538; Coverage: 58%)
Sequence domains: Calicivirus coat protein C-terminal
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: GAL, FUC
Carbohydrate polymer
2 bound ligands:
Ligand EDO 22 x EDO
Ligand IMD 4 x IMD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P21
Unit cell:
a: 65.117Å b: 78.768Å c: 69.49Å
α: 90° β: 99.93° γ: 90°
R-values:
R R work R free
0.169 0.168 0.182
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

16 review citations

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

2 mentions without citation

Crystal structures of GII.10 and GII.12 norovirus protruding domains in complex with histo-blood group antigens reveal details for a potential site of vulnerability.
Hansman et al. (2011)
1 more