3BY2

Norwalk P polypeptide (228-523)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for the receptor binding specificity of Norwalk virus.

Bu, W.Mamedova, A.Tan, M.Xia, M.Jiang, X.Hegde, R.S.

(2008) J.Virol. 82: 5340-5347

  • DOI: 10.1128/JVI.00135-08
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Noroviruses are positive-sense, single-stranded RNA viruses that cause acute gastroenteritis. They recognize human histo-blood group antigens as receptors in a strain-specific manner. The structures presented here were analyzed in order to elucidate ...

    Noroviruses are positive-sense, single-stranded RNA viruses that cause acute gastroenteritis. They recognize human histo-blood group antigens as receptors in a strain-specific manner. The structures presented here were analyzed in order to elucidate the structural basis for differences in ligand recognition of noroviruses from different genogroups, the prototypic Norwalk virus (NV; GI-1) and VA387 (GII-4), which recognize the same A antigen but differ in that NV is unable to bind to the B antigen. Two forms of the receptor-binding domain of the norovirus coat protein, the P domain and the P polypeptide, that were previously shown to differ in receptor binding and P-particle formation properties were studied. Comparison of the structures of the NV P domain with and without A trisaccharide and the NV P polypeptide revealed no major ligand-induced changes. The 2.3-A cocrystal structure reveals that the A trisaccharide binds to the NV P domain through interactions with the residues Ser377, Asp327, His329, and Ser380 in a mode distinct from that previously reported for the VA387 P-domain-A-trisaccharide complex. Mutational analyses confirm the importance of these residues in NV P-particle binding to native A antigen. The alpha-GalNAc residue unique to the A trisaccharide is buried deeply in the NV binding pocket, unlike in the structures of A and B trisaccharides bound to VA387 P domain, where the alpha-fucose residue forms the most protein contacts. The A-trisaccharide binding mode seen in the NV P domain complex cannot be sterically accommodated in the VA387 P domain.


    Organizational Affiliation

    Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
58 kd capsid protein
A
305Norwalk virus (strain GI/Human/United States/Norwalk/1968)Mutation(s): 0 
Find proteins for Q83884 (Norwalk virus (strain GI/Human/United States/Norwalk/1968))
Go to UniProtKB:  Q83884
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.212 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 82.799α = 90.00
b = 83.771β = 90.00
c = 102.229γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
CrystalCleardata collection
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-01-15 
  • Released Date: 2008-04-22 
  • Deposition Author(s): Hegde, R., Bu, W.

Revision History 

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance