PDBsum entry 2jlt

RNA

PDB id: 2jlt

Contents

DNA/RNA

PDB id:

2jlt

Name:

RNA

Title:

Crystal structure of an RNA kissing complex

Structure:

R06. Chain: a. Synonym: 5'-r( Gp Gp 5Bup Cp Gp Gp Up Cp Cp Cp Ap Gp Ap Cp Gp Ap Cp C)-3'. Engineered: yes. Tar. Chain: b. Synonym: 5'-r( Gp Gp Ap Gp Cp Cp Up Gp Gp Gp Ap Gp Cp 5Bup Cp C)-3'. Engineered: yes

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Organism_taxid: 562

Resolution:

2.90Å R-factor: 0.189 R-free: 0.227

Authors:

C.Diprimo,S.Fribourg

Key ref:

I.Lebars et al. (2008). Exploring TAR-RNA aptamer loop-loop interaction by X-ray crystallography, UV spectroscopy and surface plasmon resonance. Nucleic Acids Res, 36, 7146-7156. PubMed id: 18996893

Date:

15-Sep-08 Release date: 18-Aug-09

DNA/RNA chains

G-G-5BU-C-G-G-U-C-C-C-A-G-A-C-G-A-C-C 18 bases

G-G-A-G-C-C-U-G-G-G-A-G-C-5BU-C-C 16 bases

Nucleic Acids Res 36:7146-7156 (2008)

PubMed id: 18996893

Exploring TAR-RNA aptamer loop-loop interaction by X-ray crystallography, UV spectroscopy and surface plasmon resonance.

I.Lebars, P.Legrand, A.Aimé, N.Pinaud, S.Fribourg, C.Di Primo.

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.