Identification of a binding site for the human immunodeficiency virus type 1 nucleocapsid protein

Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):5219-23. doi: 10.1073/pnas.90.11.5219.


The nucleocapsid (NC) protein NCp7 of human immunodeficiency virus type 1 (HIV-1) is important for encapsidation of the virus genome, RNA dimerization, and primer tRNA annealing in vitro. Here we present evidence from gel mobility-shift experiments indicating that NCp7 binds specifically to an RNA sequence. Two complexes were identified in native gels. The more slowly migrating complex contained two RNA molecules and one peptide, while the more rapidly migrating one is composed of one RNA and one peptide. Further, mutational analysis of the RNA shows that the predicted stem and loop structure of stem-loop 1 plays a critical role. Our results show that NCp7 binds to a unique RNA structure within the psi region; in addition, this structure is necessary for RNA dimerization. We propose that NCp7 binds to the RNA via a direct interaction of one zinc-binding motif to stem-loop 1 followed by binding of the other zinc-binding motif to stem-loop 1, stem-loop 2, or the linker region of the second RNA molecule, forming a bridge between the two RNAs.

Publication types

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

MeSH terms

  • Base Sequence
  • Binding Sites
  • Bromodeoxyuridine
  • Capsid / genetics
  • Capsid / metabolism*
  • Cross-Linking Reagents
  • Genes, gag
  • HIV-1 / genetics
  • HIV-1 / metabolism*
  • Molecular Sequence Data
  • Mutagenesis
  • Nucleic Acid Conformation
  • Peptide Fragments / chemical synthesis
  • Peptide Fragments / metabolism
  • Protein Folding
  • RNA, Viral / chemistry
  • RNA, Viral / genetics
  • RNA, Viral / metabolism*
  • Sequence Deletion
  • Ultraviolet Rays
  • Viral Core Proteins / genetics
  • Viral Core Proteins / metabolism*
  • Zinc Fingers / genetics
  • Zinc Fingers / physiology


  • Cross-Linking Reagents
  • Peptide Fragments
  • RNA, Viral
  • Viral Core Proteins
  • Bromodeoxyuridine