1EBR

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

Summary for 1EBR

• Entry DOI: 10.2210/pdb1ebr/pdb
• Related: 1EBQ 1EBS
• Descriptor: HIV-1 REV RESPONSIVE ELEMENT RNA (1 entity in total)
• Functional Keywords: ribonucleic acid, rna
• Total number of polymer chains: 1
• Total formula weight: 9691.80

Authors

Peterson, R.D.,Feigon, J. (deposition date: 1997-03-20, release date: 1997-07-07, Last modification date: 2024-05-22)

Primary citation

Peterson, R.D.,Feigon, J.
Structural change in Rev responsive element RNA of HIV-1 on binding Rev peptide.
J.Mol.Biol., 264:863-877, 1996

PubMed Abstract: 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.

PubMed: 9000617
DOI: 10.1006/jmbi.1996.0683

Experimental method

SOLUTION NMR