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 

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.USA 111: 12781-12786

  • DOI: 10.1073/pnas.1407122111
  • Primary Citation of Related Structures:  

  • 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

    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.,Department of BioSciences, Rice University, Houston, TX 77005; ytao@rice.edu.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030; and.,Department of BioSciences, Rice University, Houston, TX 77005;,Departments of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein
A, C, B
391Orsay virusMutation(s): 0 
Find proteins for E9KNV5 (Orsay virus)
Go to UniProtKB:  E9KNV5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
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 
  • Space Group: I 2 2 2
  • Diffraction Data DOI: 
    10.15785/SBGRID/9 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 402.197α = 90.00
b = 369.862β = 90.00
c = 410.511γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
CNSrefinement
MD2data collection
RAVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references
  • Version 1.2: 2015-12-02
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Refinement description