Crystal structure of Orsay virus-like particle

Experimental Data Snapshot

  • Resolution: 3.25 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.278 

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This is version 1.3 of the entry. See complete history


Crystal structure of a nematode-infecting virus.

Guo, Y.R.Hryc, C.F.Jakana, J.Jiang, H.Wang, D.Chiu, W.Zhong, W.Tao, Y.J.

(2014) Proc Natl Acad Sci U S A 111: 12781-12786

  • DOI: https://doi.org/10.1073/pnas.1407122111
  • Primary Citation of Related Structures:  
    4NWV, 4NWW

  • PubMed Abstract: 

    Orsay, the first virus discovered to naturally infect Caenorhabditis elegans or any nematode, has a bipartite, positive-sense RNA genome. Sequence analyses show that Orsay is related to nodaviruses, but molecular characterizations of Orsay reveal several unique features, such as the expression of a capsid-δ fusion protein and the use of an ATG-independent mechanism for translation initiation. Here we report the crystal structure of an Orsay virus-like particle assembled from recombinant capsid protein (CP). Orsay capsid has a T = 3 icosahedral symmetry with 60 trimeric surface spikes. Each CP can be divided into three regions: an N-terminal arm that forms an extended protein interaction network at the capsid interior, an S domain with a jelly-roll, β-barrel fold forming the continuous capsid, and a P domain that forms surface spike projections. The structure of the Orsay S domain is best aligned to T = 3 plant RNA viruses but exhibits substantial differences compared with the insect-infecting alphanodaviruses, which also lack the P domain in their CPs. The Orsay P domain is remotely related to the P1 domain in calicivirus and hepatitis E virus, suggesting a possible evolutionary relationship. Removing the N-terminal arm produced a slightly expanded capsid with fewer nucleic acids packaged, suggesting that the arm is important for capsid stability and genome packaging. Because C. elegans-Orsay serves as a highly tractable model for studying viral pathogenesis, our results should provide a valuable structural framework for further studies of Orsay replication and infection.

  • Organizational Affiliation

    Graduate Program in Structural and Computational Biology and Molecular Biophysics and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030; and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid proteinA,
B [auth C],
C [auth B]
391Orsay virusMutation(s): 0 
Gene Names: Capsid Protein
Find proteins for E9KNV5 (Orsay virus)
Explore E9KNV5 
Go to UniProtKB:  E9KNV5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9KNV5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 402.197α = 90
b = 369.862β = 90
c = 410.511γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MD2data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2015-12-02
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Refinement description