4EWC

Crystal Structure of the Infectious Salmon Anemia Virus Nucleoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.268 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The crystal structure and RNA-binding of an orthomyxovirus nucleoprotein.

Zheng, W.Olson, J.Vakharia, V.Tao, Y.J.

(2013) Plos Pathog. 9: e1003624-e1003624

  • DOI: 10.1371/journal.ppat.1003624

  • PubMed Abstract: 
  • Genome packaging for viruses with segmented genomes is often a complex problem. This is particularly true for influenza viruses and other orthomyxoviruses, whose genome consists of multiple negative-sense RNAs encapsidated as ribonucleoprotein (RNP) ...

    Genome packaging for viruses with segmented genomes is often a complex problem. This is particularly true for influenza viruses and other orthomyxoviruses, whose genome consists of multiple negative-sense RNAs encapsidated as ribonucleoprotein (RNP) complexes. To better understand the structural features of orthomyxovirus RNPs that allow them to be packaged, we determined the crystal structure of the nucleoprotein (NP) of a fish orthomyxovirus, the infectious salmon anemia virus (ISAV) (genus Isavirus). As the major protein component of the RNPs, ISAV-NP possesses a bi-lobular structure similar to the influenza virus NP. Because both RNA-free and RNA-bound ISAV NP forms stable dimers in solution, we were able to measure the NP RNA binding affinity as well as the stoichiometry using recombinant proteins and synthetic oligos. Our RNA binding analysis revealed that each ISAV-NP binds ~12 nts of RNA, shorter than the 24-28 nts originally estimated for the influenza A virus NP based on population average. The 12-nt stoichiometry was further confirmed by results from electron microscopy and dynamic light scattering. Considering that RNPs of ISAV and the influenza viruses have similar morphologies and dimensions, our findings suggest that NP-free RNA may exist on orthomyxovirus RNPs, and selective RNP packaging may be accomplished through direct RNA-RNA interactions.


    Organizational Affiliation

    Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative nucleoprotein
A
607Infectious salmon anemia virus (isolate Atlantic salmon/Norway/810/9/99)Mutation(s): 0 
Gene Names: Segment-3
Find proteins for Q8V3T7 (Infectious salmon anemia virus (isolate Atlantic salmon/Norway/810/9/99))
Go to UniProtKB:  Q8V3T7
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.268 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 112.983α = 90.00
b = 112.983β = 90.00
c = 103.310γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-04-26 
  • Released Date: 2013-05-08 
  • Deposition Author(s): Zheng, W., Tao, Y.J.

Revision History 

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Database references