Influenza A virus nucleoprotein NP at 3.2A resolution

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.273 

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The mechanism by which influenza A virus nucleoprotein forms oligomers and binds RNA.

Ye, Q.Krug, R.M.Tao, Y.J.

(2006) Nature 444: 1078-1082

  • DOI: https://doi.org/10.1038/nature05379
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Influenza A viruses pose a serious threat to world public health, particularly the currently circulating avian H5N1 viruses. The influenza viral nucleoprotein forms the protein scaffold of the helical genomic ribonucleoprotein complexes, and has a critical role in viral RNA replication. Here we report a 3.2 A crystal structure of this nucleoprotein, the overall shape of which resembles a crescent with a head and a body domain, with a protein fold different compared with that of the rhabdovirus nucleoprotein. Oligomerization of the influenza virus nucleoprotein is mediated by a flexible tail loop that is inserted inside a neighbouring molecule. This flexibility in the tail loop enables the nucleoprotein to form loose polymers as well as rigid helices, both of which are important for nucleoprotein functions. Single residue mutations in the tail loop result in the complete loss of nucleoprotein oligomerization. An RNA-binding groove, which is found between the head and body domains at the exterior of the nucleoprotein oligomer, is lined with highly conserved basic residues widely distributed in the primary sequence. The nucleoprotein structure shows that only one of two proposed nuclear localization signals are accessible, and suggests that the body domain of nucleoprotein contains the binding site for the viral polymerase. Our results identify the tail loop binding pocket as a potential target for antiviral development.

  • Organizational Affiliation

    Department of Biochemistry and Cell Biology, Rice University, 6100 Main Street, MS140, Houston, Texas 77005, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleocapsid protein
A, B, C
499Influenza A virus (A/Wilson-Smith/1933(H1N1))Mutation(s): 0 
Gene Names: NP
Find proteins for Q1K9H2 (Influenza A virus (strain A/Wilson-Smith/1933 H1N1))
Explore Q1K9H2 
Go to UniProtKB:  Q1K9H2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1K9H2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.273 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.099α = 90
b = 135.105β = 90
c = 195.183γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references