DSSR-PyMOL cartoon-block schematics: PDB entry 2l8f

PDB-id

2l8f; DSSR-derived features in text and JSON formats

Class

RNA

Method

NMR

Summary

Structure of a 4x4 nucleotide RNA internal loop from an r2 retrotransposon

Reference

Lerman YV, Kennedy SD, Shankar N, Parisien M, Major F, Turner DH (2011): "NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: Identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions." Rna, 17, 1664-1677. doi: 10.1261/rna.2641911.

Abstract

The NMR solution structure is reported of a duplex, 5'GUGAAGCCCGU/3'UCACAGGAGGC, containing a 4 × 4 nucleotide internal loop from an R2 retrotransposon RNA. The loop contains three sheared purine-purine pairs and reveals a structural element found in other RNAs, which we refer to as the 3RRs motif. Optical melting measurements of the thermodynamics of the duplex indicate that the internal loop is 1.6 kcal/mol more stable at 37°C than predicted. The results identify the 3RRs motif as a common structural element that can facilitate prediction of 3D structure. Known examples include internal loops having the pairings: 5'GAA/3'AGG, 5'GAG/3'AGG, 5'GAA/3'AAG, and 5'AAG/3'AGG. The structural information is compared with predictions made with the MC-Sym program.