1K9W

HIV-1(MAL) RNA Dimerization Initiation Site

Summary for 1K9W

• Entry DOI: 10.2210/pdb1k9w/pdb
• Related: 1JJM 1JJN
• Descriptor: HIV-1 DIS(Mal)UU RNA, MAGNESIUM ION (2 entities in total)
• Functional Keywords: hiv, rna, hairpin
• Total number of polymer chains: 4
• Total formula weight: 29554.88

Authors

Ennifar, E.,Walter, P.,Ehresmann, B.,Ehresmann, C.,Dumas, P. (deposition date: 2001-10-31, release date: 2001-11-30, Last modification date: 2024-02-07)

Primary citation

Ennifar, E.,Walter, P.,Ehresmann, B.,Ehresmann, C.,Dumas, P.
Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site.
Nat.Struct.Biol., 8:1064-1068, 2001

PubMed Abstract: We describe the crystal structures of the RNA dimerization initiation sites (DIS) of HIV-1 subtypes A and B. Both molecules adopt a hairpin conformation, with loop sequences consisting of 272-AGGUGCACA-280 and 272-AAGCGCGCA-280, respectively. This includes a six-base self-complementary stretch (underlined) that allows homodimerization through the formation of a loop-loop, or 'kissing-loop', complex. The DISs for the two sequences have identical conformations, and the two interacting hairpins show a perfect coaxial alignment. The conserved purines, A272 and R273, are stacked in a bulged-out conformation and symmetrically join the upward and downward strands of each hairpin by crossing the helix major groove. There is good agreement between these structures and previous results from chemical probing in solution, as well as with differences in magnesium dependence for dimerization. The overall shape of the kissing-loop complex is very similar to that of the previously determined subtype A DIS duplex form. Unexpectedly, the purine R273 is the only base seen at a different position and is responsible for the difference in topology between the two forms. We propose that the transition from kissing-loop duplex could occur by a recombination mechanism based on symmetrical chain cleavage at R273 of each hairpin and subsequent cross-religation, rather than by base-pair melting and subsequent reannealing.

PubMed: 11702070
DOI: 10.1038/nsb727

Experimental method

X-RAY DIFFRACTION (3.1 Å)