2OIY

Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site

Summary for 2OIY

• Entry DOI: 10.2210/pdb2oiy/pdb
• Related: 1Y99 2OIJ 2OJ0 462D
• Descriptor: 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP*GP*CP*AP*AP*G)-3', POTASSIUM ION, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: hiv-1, dis, rna, dimerization
• Total number of polymer chains: 2
• Total formula weight: 15000.88

Authors

Ennifar, E.,Walter, P.,Dumas, P. (deposition date: 2007-01-12, release date: 2007-12-25, Last modification date: 2023-12-27)

Primary citation

Ennifar, E.,Walter, P.,Dumas, P.
Cation-dependent cleavage of the duplex form of the subtype-B HIV-1 RNA dimerization initiation site.
Nucleic Acids Res., 38:5807-5816, 2010

PubMed Abstract: The crystal structure of subtype-B HIV-1 genomic RNA Dimerization Initiation Site duplex revealed chain cleavage at a specific position resulting in 3'-phosphate and 5'-hydroxyl termini. A crystallographic analysis showed that Ba(2+), Mn(2+), Co(2+) and Zn(2+) bind specifically on a guanine base close to the cleaved position. The crystal structures also point to a necessary conformational change to induce an 'in-line' geometry at the cleavage site. In solution, divalent cations increased the rate of cleavage with pH/pKa compensation, indicating that a cation-bound hydroxide anion is responsible for the cleavage. We propose a 'Trojan horse' mechanism, possibly of general interest, wherein a doubly charged cation hosted near the cleavage site as a 'harmless' species is further transformed in situ into an 'aggressive' species carrying a hydroxide anion.

PubMed: 20460458
DOI: 10.1093/nar/gkq344

Experimental method

X-RAY DIFFRACTION (1.6 Å)