247d

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spinqualitylabelsall models 247d, resolution 2.800Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

CRYSTAL STRUCTURES OF AN A-FORM DUPLEX WITH SINGLE-ADENOSINE BULGES AND A CONFORMATIONAL BASIS FOR SITE SPECIFIC RNA SELF-CLEAVAGE

Overview

BACKGROUND: Bulged nucleotides are common secondary structural motifs in, RNA molecules and are often involved in RNA-RNA and RNA-protein, interactions. RNA is selectively cleaved at bulge sites (when compared to, other sites within stems) in the presence of divalent metal cations. The, effects of bulge nucleotides on duplex stability and topology have been, extensively investigated, but no detailed X-ray structures of, bulge-containing RNA fragments have been available. RESULTS: We have, crystallized a self-complementary RNA-DNA chimeric 11-nucleotide sequence, containing single-adenosine bulges under two different conditions, giving, two distinct crystal forms. In both lattices the adenosines are looped, out, leaving the stacking interactions in the duplex virtually unaffected., The bulges cause the duplex to kink in both cases. In one of the, structures, the conformation of the bulged nucleotide places its modeled, 2'-oxygen in line with the adjacent phosphate on the 3' side, where it is, poised for nucleophilic attack. CONCLUSIONS: Single adenosine bulges cause, a marked opening of the normally narrow RNA major groove in both crystal, structures, rendering the bases more accessible to interacting molecules, compared with an intact stem. The geometries around the looped-out, adenosines are different in the two crystal forms, indicating that bulges, can confer considerable local plasticity on the usually rigid RNA double, helix. The results provide a conformational basis for the preferential, metal-assisted self-cleavage of RNA at bulged sites.

About this Structure

247D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage., Portmann S, Grimm S, Workman C, Usman N, Egli M, Chem Biol. 1996 Mar;3(3):173-84. PMID:8807843

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