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 several unique features, such as the expression of a capsid-δ fusion protein and the use of an ATG-independent mechanism for translation initiation ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid proteinA,
C [auth B],
B [auth C]
391Orsay virusMutation(s): 0 
Gene Names: Capsid Protein
UniProt
Find proteins for E9KNV5 (Orsay virus)
Explore E9KNV5 
Go to UniProtKB:  E9KNV5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9KNV5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth 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  (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