Structure of the HIV-1 nucleocapsid protein bound to the SL3 ψ-RNA recognition element

The three-dimensional structure of the human immunodeficiency virus- type 1 (HIV-1) nucleocapsid protein (NC) bound to the SL3 stem-loop recognition element of the genomic Ψ RNA packaging signal has been determined by heteronuclear magnetic resonance spectroscopy. Tight binding (dissociation constant, ~100 nM) is mediated by specific interactions between the amino- and carboxyl-terminal CCHC-type zinc knuckles of the NC protein and the G⁷ and G⁹ nucleotide bases, respectively, of the G⁶-G⁷- A⁸-G⁹ RNA tetraloop. A⁸ packs against the amino-terminal knuckle and forms a hydrogen bond with conserved Arg³², and residues Lys³ to Arg¹⁰ of NC form a 3₁₀ helix that binds to the major groove of the RNA stem and also packs against the amino-terminal zinc knuckle. The structure provides insights into the mechanism of viral genome recognition, explains extensive amino acid conservation within NC, and serves as a basis for the development of inhibitors designed to interfere with genome encapsidation.