1A1T

STRUCTURE OF THE HIV-1 NUCLEOCAPSID PROTEIN BOUND TO THE SL3 PSI-RNA RECOGNITION ELEMENT, NMR, 25 STRUCTURES

Summary for 1A1T

• Entry DOI: 10.2210/pdb1a1t/pdb
• Descriptor: SL3 STEM-LOOP RNA, NUCLEOCAPSID PROTEIN, ZINC ION (3 entities in total)
• Functional Keywords: nucleocapsid protein, complex (nucleocapsid protein-rna), stem-loop rna, viral protein-rna complex, viral protein/rna
• Biological source: Human immunodeficiency virus 1
• Total number of polymer chains: 2
• Total formula weight: 12995.23

Authors

De Guzman, R.N.,Wu, Z.R.,Stalling, C.C.,Pappalardo, L.,Borer, P.N.,Summers, M.F. (deposition date: 1997-12-15, release date: 1998-06-17, Last modification date: 2024-05-22)

Primary citation

De Guzman, R.N.,Wu, Z.R.,Stalling, C.C.,Pappalardo, L.,Borer, P.N.,Summers, M.F.
Structure of the HIV-1 nucleocapsid protein bound to the SL3 psi-RNA recognition element.
Science, 279:384-388, 1998

PubMed Abstract: 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 Psi RNA packaging signal has been determined by heteronuclear magnetic resonance spectroscopy. Tight binding (dissociation constant, approximately 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.

PubMed: 9430589
DOI: 10.1126/science.279.5349.384

Experimental method

SOLUTION NMR