2JLT

Crystal structure of an RNA kissing complex

Summary for 2JLT

• Entry DOI: 10.2210/pdb2jlt/pdb
• Descriptor: R06, TAR (2 entities in total)
• Functional Keywords: rna, kissing complex
• Biological source: ESCHERICHIA COLI; More
• Total number of polymer chains: 2
• Total formula weight: 11088.42

Authors

DiPrimo, C.,Fribourg, S. (deposition date: 2008-09-15, release date: 2009-08-18, Last modification date: 2024-05-08)

Primary citation

Lebars, I.,Legrand, P.,Aime, A.,Pinaud, N.,Fribourg, S.,Di Primo, C.
Exploring Tar-RNA Aptamer Loop-Loop Interaction by X-Ray Crystallography, Uv Spectroscopy and Surface Plasmon Resonance.
Nucleic Acids Res., 36:7146-, 2008

PubMed Abstract: In HIV-1, trans-activation of transcription of the viral genome is regulated by an imperfect hairpin, the trans-activating responsive (TAR) RNA element, located at the 5' untranslated end of all viral transcripts. TAR acts as a binding site for viral and cellular proteins. In an attempt to identify RNA ligands that would interfere with the virus life-cycle by interacting with TAR, an in vitro selection was previously carried out. RNA hairpins that formed kissing-loop dimers with TAR were selected [Ducongé F. and Toulmé JJ (1999) RNA, 5:1605-1614]. We describe here the crystal structure of TAR bound to a high-affinity RNA aptamer. The two hairpins form a kissing complex and interact through six Watson-Crick base pairs. The complex adopts an overall conformation with an inter-helix angle of 28.1 degrees , thus contrasting with previously reported solution and modelling studies. Structural analysis reveals that inter-backbone hydrogen bonds between ribose 2' hydroxyl and phosphate oxygens at the stem-loop junctions can be formed. Thermal denaturation and surface plasmon resonance experiments with chemically modified 2'-O-methyl incorporated into both hairpins at key positions, clearly demonstrate the involvement of this intermolecular network of hydrogen bonds in complex stability.

PubMed: 18996893
DOI: 10.1093/NAR/GKN831

Experimental method

X-RAY DIFFRACTION (2.9 Å)