4Z4W

Crystal structure of GII.10 P domain in complex with 4.7mM fucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The sweet quartet: Binding of fucose to the norovirus capsid.

Koromyslova, A.D.Leuthold, M.M.Bowler, M.W.Hansman, G.S.

(2015) Virology 483: 203-208

  • DOI: 10.1016/j.virol.2015.04.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human noroviruses bind histo-blood group antigens (HBGAs) and this interaction is thought to be important for an infection. We identified two additional fucose-binding pockets (termed fucose-3/4 sites) on a genogroup II human (GII.10) norovirus-protr ...

    Human noroviruses bind histo-blood group antigens (HBGAs) and this interaction is thought to be important for an infection. We identified two additional fucose-binding pockets (termed fucose-3/4 sites) on a genogroup II human (GII.10) norovirus-protruding (P) dimer using X-ray crystallography. Fucose-3/4 sites were located between two previously determined HBGA binding pockets (termed fucose-1/2 sites). We found that four fucose molecules were capable of binding altogether at fucose-1/2/3/4 sites on the P dimer, though the fucose molecules bound in a dose-dependent and step-wise manner. We also showed that HBGA B-trisaccharide molecules bound in a similar way at the fucose-1/2 sites. Interestingly, we discovered that the monomers of the P dimer were asymmetrical in an unliganded state and when a single B-trisaccharide molecule bound, but were symmetrical when two B-trisaccharide molecules bound. We postulate that the symmetrical dimers might favor HBGA binding interactions at fucose-1/2 sites.


    Organizational Affiliation

    Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg 69120, Germany; Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg 69120, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein
A, B
315Norwalk virusMutation(s): 0 
Find proteins for Q5F4T5 (Norwalk virus)
Go to UniProtKB:  Q5F4T5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FUL
Query on FUL

Download SDF File 
Download CCD File 
A
BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.155 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.290α = 90.00
b = 79.344β = 100.78
c = 69.576γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 1.1: 2015-06-03
    Type: Database references