2OBR

Crystal Structures of P Domain of Norovirus VA387


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural basis for the recognition of blood group trisaccharides by norovirus.

Cao, S.Lou, Z.Tan, M.Chen, Y.Liu, Y.Zhang, Z.Zhang, X.C.Jiang, X.Li, X.Rao, Z.

(2007) J Virol 81: 5949-5957

  • DOI: https://doi.org/10.1128/JVI.00219-07
  • Primary Citation of Related Structures:  
    2OBR, 2OBS, 2OBT

  • PubMed Abstract: 

    Noroviruses are one of the major causes of nonbacterial gastroenteritis epidemics in humans. Recent studies on norovirus receptors show that different noroviruses recognize different human histo-blood group antigens (HBGAs), and eight receptor binding patterns of noroviruses have been identified. The P domain of the norovirus capsids is directly involved in this recognition. To determine the precise locations and receptor binding modes of HBGA carbohydrates on the viral capsids, a recombinant P protein of a GII-4 strain norovirus, VA387, was cocrystallized with synthetic type A or B trisaccharides. Based on complex crystal structures observed at a 2.0-A resolution, we demonstrated that the receptor binding site lies at the outermost end of the P domain and forms an extensive hydrogen-bonding network with the saccharide ligand. The A and B trisaccharides display similar binding modes, and the common fucose ring plays a key role in this interaction. The extensive interface between the two protomers in a P dimer also plays a crucial role in the formation of the receptor binding interface.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein327NorovirusMutation(s): 2 
UniProt
Find proteins for Q913Z3 (Human calicivirus NLV/VA98387/1998)
Explore Q913Z3 
Go to UniProtKB:  Q913Z3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ913Z3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.333α = 90
b = 97.439β = 90
c = 118.912γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
CNSrefinement
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2021-11-10
    Changes: Database references
  • Version 1.5: 2023-10-25
    Changes: Data collection, Refinement description