The solution structure of HIV-1 Nef reveals an unexpected fold and permits delineation of the binding surface for the SH3 domain of Hck tyrosine protein kinase

Nat Struct Biol. 1996 Apr;3(4):340-5. doi: 10.1038/nsb0496-340.


The solution structure of HIV-1 Nef has been solved by multidimensional heteronuclear NMR spectroscopy. The construct employed to circumvent problems associated with aggregation was a double-deletion mutant (delta2-39, delta159-173) in which conformationally disordered regions of the protein at the N terminus and in a long solvent-exposed flexible loop were removed, without affecting the properties or structural integrity of the remainder of the protein. Despite the absence of any sequence similarity, the overall fold of Nef is reminiscent of that of the family of winged helix-turn-helix DNA binding proteins. The binding surface of Nef for the SH3 domain of Hck tyrosine protein kinase has been mapped and reveals a non-contiguous (in terms of amino-acid sequence) interaction surface. This unique feature may suggest possible avenues for drug design aimed at inhibiting the interaction between Nef and SH3 domains.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Gene Products, nef / chemistry*
  • Gene Products, nef / metabolism
  • HIV-1 / chemistry*
  • Helix-Turn-Helix Motifs
  • Humans
  • Magnetic Resonance Spectroscopy / methods
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Folding
  • Protein Structure, Secondary
  • Protein-Tyrosine Kinases / chemistry
  • Protein-Tyrosine Kinases / metabolism*
  • Proto-Oncogene Proteins / chemistry
  • Proto-Oncogene Proteins / metabolism*
  • Proto-Oncogene Proteins c-hck
  • Sequence Deletion
  • nef Gene Products, Human Immunodeficiency Virus
  • src Homology Domains*


  • Gene Products, nef
  • Proto-Oncogene Proteins
  • nef Gene Products, Human Immunodeficiency Virus
  • Protein-Tyrosine Kinases
  • HCK protein, human
  • Proto-Oncogene Proteins c-hck