1sdr
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(New page: 200px<br /><applet load="1sdr" size="450" color="white" frame="true" align="right" spinBox="true" caption="1sdr, resolution 2.600Å" /> '''CRYSTAL STRUCTURE O...)
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CRYSTAL STRUCTURE OF AN RNA DODECAMER CONTAINING THE ESCHERICHIA COLI SHINE-DALGARNO SEQUENCE
Overview
The synthetic dodecameric RNA fragment rUAAGGAGGUGAU resembles a region, upstream of the initiation site in prokaryotic mRNAs whereas the, pyrimidine-rich complementary strand is identical to the last 12, nucleotides of Escherichia coli 16 S rRNA. The complex thus serves as a, model for the Shine-Dalgarno interaction which is required for proper, initiation of translation. The crystal structure of, rUAAGGAGGUGUA.rAUCACCUCCUUA has been determined at 2.6 A resolution and, refined against 2957 1 sigma(F) structure amplitudes to an R-value of, 0.195. The unit cell of the triclinic crystals contains two, double-stranded RNA molecules. The conformation of the two duplexes is, similar, with a root-mean-square deviation of 0.683 A between equivalent, atoms, and resembles calf thymus A-DNA as determined by X-ray fiber, diffraction methods. Both molecules from continuous helices that penetrate, the entire crystal, but the dinucleotide step in between dodecameric, duplexes has an unusual geometry with a negative twist angle. The long, helices cross over each other in a characteristic manner by inserting the, backbone of one molecule into the minor groove of another. These contacts, are stabilized by several direct intermolecular hydrogen bonds most of, which are mediated by 2'-hydroxyl groups of the ribose sugars suggesting a, general mode for the interaction between RNA molecules which is different, from DNA-DNA interactions.
About this Structure
1SDR is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Crystal structure of an RNA dodecamer containing the Escherichia coli Shine-Dalgarno sequence., Schindelin H, Zhang M, Bald R, Furste JP, Erdmann VA, Heinemann U, J Mol Biol. 1995 Jun 9;249(3):595-603. PMID:7540215
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