Structural basis for suppression of a host antiviral response by influenza A virus

Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):13093-8. doi: 10.1073/pnas.0805213105. Epub 2008 Aug 25.


Influenza A viruses are responsible for seasonal epidemics and high mortality pandemics. A major function of the viral NS1A protein, a virulence factor, is the inhibition of the production of IFN-beta mRNA and other antiviral mRNAs. The NS1A protein of the human influenza A/Udorn/72 (Ud) virus inhibits the production of these antiviral mRNAs by binding the cellular 30-kDa subunit of the cleavage and polyadenylation specificity factor (CPSF30), which is required for the 3' end processing of all cellular pre-mRNAs. Here we report the 1.95-A resolution X-ray crystal structure of the complex formed between the second and third zinc finger domain (F2F3) of CPSF30 and the C-terminal domain of the Ud NS1A protein. The complex is a tetramer, in which each of two F2F3 molecules wraps around two NS1A effector domains that interact with each other head-to-head. This structure identifies a CPSF30 binding pocket on NS1A comprised of amino acid residues that are highly conserved among human influenza A viruses. Single amino acid changes within this binding pocket eliminate CPSF30 binding, and a recombinant Ud virus expressing an NS1A protein with such a substitution is attenuated and does not inhibit IFN-beta pre-mRNA processing. This binding pocket is a potential target for antiviral drug development. The crystal structure also reveals that two amino acids outside of this pocket, F103 and M106, which are highly conserved (>99%) among influenza A viruses isolated from humans, participate in key hydrophobic interactions with F2F3 that stabilize the complex.

Publication types

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

MeSH terms

  • Amino Acid Substitution
  • Binding Sites
  • Cell Line
  • Crystallography, X-Ray
  • Humans
  • Influenza A virus / chemistry*
  • Influenza A virus / immunology*
  • Interferon Regulatory Factor-3 / metabolism
  • Methionine / metabolism
  • Models, Molecular
  • Phenylalanine / metabolism
  • Protein Structure, Quaternary
  • Protein Structure, Secondary
  • Thermodynamics
  • Viral Nonstructural Proteins / chemistry
  • Viral Nonstructural Proteins / metabolism
  • Zinc Fingers


  • Interferon Regulatory Factor-3
  • Viral Nonstructural Proteins
  • Phenylalanine
  • Methionine

Associated data

  • PDB/2RHK