2b8r

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spinqualitylabelsall models 2b8r, resolution 2.60Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Structure oF HIV-1(LAI) genomic RNA DIS

Overview

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.

About this Structure

2B8R is a Protein complex structure of sequences from [1] with MG, SO4 and NA as ligands. This structure superseeds the now removed PDB entry 1JJM. Full crystallographic information is available from OCA.

Reference

Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site., Ennifar E, Walter P, Ehresmann B, Ehresmann C, Dumas P, Nat Struct Biol. 2001 Dec;8(12):1064-8. PMID:11702070

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