Structure of the P domain from a GI.7 Norovirus variant in complex with A-type 2 HBGA

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

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Structural analysis of determinants of histo-blood group antigen binding specificity in genogroup I noroviruses.

Shanker, S.Czako, R.Sankaran, B.Atmar, R.L.Estes, M.K.Prasad, B.V.

(2014) J Virol 88: 6168-6180

  • DOI: https://doi.org/10.1128/JVI.00201-14
  • Primary Citation of Related Structures:  
    4P12, 4P1V, 4P25, 4P26, 4P2N, 4P3I

  • PubMed Abstract: 

    Human noroviruses (NoVs) cause acute epidemic gastroenteritis. Susceptibility to the majority of NoV infections is determined by genetically controlled secretor-dependent expression of histo-blood group antigens (HBGAs), which are also critical for NoV attachment to host cells. Human NoVs are classified into two major genogroups (genogroup I [GI] and GII), with each genogroup further divided into several genotypes. GII NoVs are more prevalent and exhibit periodic emergence of new variants, suggested to be driven by altered HBGA binding specificities and antigenic drift. Recent epidemiological studies show increased activity among GI NoVs, with some members showing the ability to bind nonsecretor HBGAs. NoVs bind HBGAs through the protruding (P) domain of the major capsid protein VP1. GI NoVs, similar to GII, exhibit significant sequence variations in the P domain; it is unclear how these variations affect HBGA binding specificities. To understand the determinants of possible strain-specific HBGA binding among GI NoVs, we determined the structure of the P domain of a GI.7 clinical isolate and compared it to the previously determined P domain structures of GI.1 and GI.2 strains. Our crystallographic studies revealed significant structural differences, particularly in the loop regions of the GI.7 P domain, altering its surface topography and electrostatic landscape and potentially indicating antigenic variation. The GI.7 strain bound to H- and A-type, Lewis secretor, and Lewis nonsecretor families of HBGAs, allowing us to further elucidate the structural determinants of nonsecretor HBGA binding among GI NoVs and to infer several contrasting and generalizable features of HBGA binding in the GI NoVs.

  • Organizational Affiliation

    Verna Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
P domain of VP1
A, B, C, D
301Norovirus Hu/GI.7/TCH-060/USA/2003Mutation(s): 0 
Find proteins for G8FL04 (Norovirus Hu/GI.7/TCH-060/USA/2003)
Explore G8FL04 
Go to UniProtKB:  G8FL04
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG8FL04
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
E, F, G
Glycosylation Resources
GlyTouCan:  G74353FF
GlyCosmos:  G74353FF
GlyGen:  G74353FF
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.58α = 99.25
b = 63.26β = 97.82
c = 90.43γ = 119.62
Software Package:
Software NamePurpose

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United States--
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-05-21
    Changes: Database references
  • Version 2.0: 2019-11-27
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 3.1: 2020-08-05
    Changes: Derived calculations, Structure summary
  • Version 3.2: 2023-09-27
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary