X-ray structure of a native calicivirus

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 

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This is version 1.4 of the entry. See complete history


X-ray structure of a native calicivirus: Structural insights into antigenic diversity and host specificity.

Chen, R.Neill, J.D.Estes, M.K.Prasad, B.V.

(2006) Proc Natl Acad Sci U S A 103: 8048-8053

  • DOI: https://doi.org/10.1073/pnas.0600421103
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Caliciviruses, grouped into four genera, are important human and veterinary pathogens with a potential for zoonosis. In these viruses, capsid-related functions such as assembly, antigenicity, and receptor interactions are predominantly encoded in a single protein that forms an icosahedral capsid. Understanding of the immunologic functions and pathogenesis of human caliciviruses in the Norovirus and Sapovirus genera is hampered by the lack of a cell culture system or animal models. Much of our understanding of these viruses, including the structure, has depended on recombinant capsids. Here we report the atomic structure of a native calicivirus from the Vesivirus genus that exhibits a broad host range possibly including humans and map immunological function onto a calicivirus structure. The vesivirus structure, despite a similar architectural design as seen in the recombinant norovirus capsid, exhibits novel features and indicates how the unique modular organization of the capsid protein with interdomain flexibility, similar to an antibody structure with a hinge and an elbow, integrates capsid-related functions and facilitates strain diversity in caliciviruses. The internally located N-terminal arm participates in a novel network of interactions through domain swapping to assist the assembly of the shell domain into an icosahedral scaffold, from which the protruding domain emanates. Neutralization epitopes localize to three hypervariable loops in the distal portion of the protruding domain surrounding a region that exhibits host-specific conservation. These observations suggest a mechanism for antigenic diversity and host specificity in caliciviruses and provide a structural framework for vaccine development.

  • Organizational Affiliation

    Verna and Marrs McLean Department of Biochemistry and Molecular Biology , Baylor College of Medicine, Houston, TX 77030, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein
A, B, C
558San Miguel sea lion virus 4Mutation(s): 0 
Find proteins for P36285 (San Miguel sea lion virus serotype 4)
Explore P36285 
Go to UniProtKB:  P36285
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36285
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 457.553α = 90
b = 457.553β = 90
c = 457.553γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SCALEPACKdata scaling
RAVEmodel building

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2006-05-16 
  • Deposition Author(s): Chen, R.

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-16
    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: 2024-02-14
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description