2IQH

Influenza A virus nucleoprotein NP at 3.2A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.271 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1038/nature05379

  • 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 cr ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleocapsid protein
A, B, C
499Influenza A virus (strain A/Wilson-Smith/1933 H1N1)Mutation(s): 0 
Gene Names: NP
Find proteins for Q1K9H2 (Influenza A virus (strain A/Wilson-Smith/1933 H1N1))
Go to UniProtKB:  Q1K9H2
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.271 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 122.099α = 90.00
b = 135.105β = 90.00
c = 195.183γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
ADSCdata collection
SHARPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-10-13 
  • Released Date: 2006-12-26 
  • Deposition Author(s): Ye, Q., Tao, Y.J.

Revision History 

  • Version 1.0: 2006-12-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance