1ebq

From Proteopedia

Revision as of 13:42, 15 February 2008

STRUCTURE OF RNA (5'-GGUGGGCGCAGCUUCGGCUGCGGUACCAC-3'), NMR, 5 STRUCTURES

Overview

The HIV-1 Rev responsive element (RRE) high-affinity binding site was, studied by homonuclear and heteronuclear NMR. Two Rev binding element, (RBE) RNA oligonucleotides were used as model systems in this study: RBE3, which contains the wild-type Rev high-affinity binding site, and RBE3-A, which is identical except for the deletion of a bulged A. The temperature, dependence of the two-dimensional spectra of the free RNAs indicates that, at lower temperatures more than one conformation is present. However, at, higher temperatures a single conformation predominates. Model structures, of RBE3 and RBE3-A as well as the RBE3-A complexed with a peptide derived, from the RNA binding domain of HIV-1 Rev, were calculated using, NMR-derived restraints. The Rev high-affinity binding site of the HIV-1, RRE contains a structured internal loop with two purine-purine base-pairs, and an extrahelical U. Comparison of the free and bound RNA structures, reveals that upon peptide binding there is a distinct change in the, backbone at G24, which is involved in a G-G base-pair. In the free RNA, G24 is in the syn conformation, and the backbone is in a relatively normal, configuration, antiparallel to the other strand. In the bound RNA, the, backbone at G24 has flipped over so that it is parallel to the other, strand. G24 in the bound RNA still forms a base-pair with G6, but is now, in the anti conformation.

About this Structure

1EBQ is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

Structural change in Rev responsive element RNA of HIV-1 on binding Rev peptide., Peterson RD, Feigon J, J Mol Biol. 1996 Dec 20;264(5):863-77. PMID:9000617

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