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

Nature. 2006 Dec 21;444(7122):1078-82. doi: 10.1038/nature05379. Epub 2006 Dec 6.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Crystallography, X-Ray
  • Influenza A virus / chemistry*
  • Influenza A virus / genetics
  • Influenza A virus / metabolism*
  • Influenza A virus / ultrastructure
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleocapsid Proteins
  • Nucleoproteins / chemistry*
  • Nucleoproteins / metabolism*
  • Nucleoproteins / ultrastructure
  • Pliability
  • Protein Structure, Secondary
  • Protein Subunits / chemistry
  • Protein Subunits / metabolism
  • RNA / genetics
  • RNA / metabolism*
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / metabolism*
  • RNA-Binding Proteins / ultrastructure
  • Static Electricity
  • Viral Core Proteins / chemistry*
  • Viral Core Proteins / metabolism*
  • Viral Core Proteins / ultrastructure


  • NP protein, Influenza A virus
  • Nucleocapsid Proteins
  • Nucleoproteins
  • Protein Subunits
  • RNA-Binding Proteins
  • Viral Core Proteins
  • RNA

Associated data

  • PDB/2IQH