Crystal Structure of the Infectious Salmon Anemia Virus Nucleoprotein

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.268 

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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: https://doi.org/10.1371/journal.ppat.1003624
  • Primary Citation of Related Structures:  

  • 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) 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative nucleoprotein607Isavirus salarisMutation(s): 0 
Find proteins for Q8V3T7 (Infectious salmon anemia virus (isolate Atlantic salmon/Norway/810/9/99))
Explore Q8V3T7 
Go to UniProtKB:  Q8V3T7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8V3T7
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.268 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.983α = 90
b = 112.983β = 90
c = 103.31γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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