5JIE

Crystal structure of the Orsay virus delta protein N-terminal fragment (aa 1~66)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1374 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of a pentameric virion-associated fiber with a potential role in Orsay virus entry to host cells.

Fan, Y.Guo, Y.R.Yuan, W.Zhou, Y.Holt, M.V.Wang, T.Demeler, B.Young, N.L.Zhong, W.Tao, Y.J.

(2017) PLoS Pathog. 13: e1006231-e1006231

  • DOI: 10.1371/journal.ppat.1006231

  • PubMed Abstract: 
  • Despite the wide use of Caenorhabditis elegans as a model organism, the first virus naturally infecting this organism was not discovered until six years ago. The Orsay virus and its related nematode viruses have a positive-sense RNA genome, encoding ...

    Despite the wide use of Caenorhabditis elegans as a model organism, the first virus naturally infecting this organism was not discovered until six years ago. The Orsay virus and its related nematode viruses have a positive-sense RNA genome, encoding three proteins: CP, RdRP, and a novel δ protein that shares no homology with any other proteins. δ can be expressed either as a free δ or a CP-δ fusion protein by ribosomal frameshift, but the structure and function of both δ and CP-δ remain unknown. Using a combination of electron microscopy, X-ray crystallography, computational and biophysical analyses, here we show that the Orsay δ protein forms a ~420-Å long, pentameric fiber with an N-terminal α-helical bundle, a β-stranded filament in the middle, and a C-terminal head domain. The pentameric nature of the δ fiber has been independently confirmed by both mass spectrometry and analytical ultracentrifugation. Recombinant Orsay capsid containing CP-δ shows protruding long fibers with globular heads at the distal end. Mutant viruses with disrupted CP-δ fibers were generated by organism-based reverse genetics. These viruses were found to be either non-viable or with poor infectivity according to phenotypic and qRT-PCR analyses. Furthermore, addition of purified δ proteins to worm culture greatly reduced Orsay infectivity in a sequence-specific manner. Based on the structure resemblance between the Orsay CP-δ fiber and the fibers from reovirus and adenovirus, we propose that CP-δ functions as a cell attachment protein to mediate Orsay entry into worm intestine cells.


    Organizational Affiliation

    Department of BioSciences, Rice University, MS-140, Houston, Texas, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein delta
B, C, E, D, A
66Orsay virusMutation(s): 0 
Find proteins for E9KNV6 (Orsay virus)
Go to UniProtKB:  E9KNV6
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1374 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 175.013α = 90.00
b = 32.133β = 99.71
c = 65.648γ = 90.00
Software Package:
Software NamePurpose
AutoSolphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-04-05
    Type: Database references