4NWV

Crystal structure of Orsay virus-like particle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.278 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 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 sev ...

    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

    Department of BioSciences, Rice University, Houston, TX 77005; ytao@rice.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid proteinABC391Orsay virusMutation(s): 0 
Gene Names: Capsid Protein
Find proteins for E9KNV5 (Orsay virus)
Explore E9KNV5 
Go to UniProtKB:  E9KNV5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.278 
  • Space Group: I 2 2 2
  • Diffraction Data DOI: 10.15785/SBGRID/9 SBGrid
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
CNSrefinement
PDB_EXTRACTdata extraction
MD2data collection
HKL-2000data reduction
HKL-2000data scaling
RAVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-12-06 
  • Released Date: 2014-08-20 
  • Deposition Author(s): Tao, Y.J., Guo, Y.R.

Revision History 

  • 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