DSSR-PyMOL cartoon-block schematics: PDB entry 1slp

PDB-id

1slp; DSSR-derived features in text and JSON formats

Class

RNA

Method

NMR

Summary

First stem loop of the sl1 RNA from caenorhabditis elegans, NMR, 16 structures

Reference

Greenbaum NL, Radhakrishnan I, Patel DJ, Hirsh D (1996): "Solution structure of the donor site of a trans-splicing RNA." Structure, 4, 725-733. doi: 10.1016/S0969-2126(96)00078-0.

Abstract

Background: RNA splicing is both ubiquitous and essential for the maturation of precursor mRNA molecules in eukaryotes. The process of trans-splicing involves the transfer of a short spliced leader (SL) RNA sequence to a consensus acceptor site on a separate pre-mRNA transcript. In Caenorhabditis elegans, a majority of pre-mRNA transcripts receive the 22-nucleotide SL from the SL1 RNA. Very little is known about the various roles that RNA structures play in the complex conformational rearrangements and reactions involved in premRNA splicing.
Results: We have determined the solution structure of a domain of the first stem loop of the SL1 RNA of C. elegans, using homonuclear and heteronuclear NMR techniques; this domain contains the splice-donor site and a nine-nucleotide hairpin loop. In solution, the SL1 RNA fragment adopts a stem-loop structure: nucleotides in the stem region form a classical A-type helix while nucleotides in the hairpin loop specify a novel conformation that includes a helix, that extends for the first three residues; a syn guanosine nucleotide at the turn region; and an extrahelical adenine that defines a pocket with nucleotides at the base of the loop.