1j9h

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Revision as of 21:11, 24 November 2007

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spinqualitylabelsall models 1j9h, resolution 1.4Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Crystal Structure of an RNA Duplex with Uridine Bulges

Overview

The crystal structure of a nonamer RNA duplex with a uridine bulge in each, strand, r(gugucgcac)(2), was determined at 1.4 A resolution. The structure, was solved by multiple anomalous diffraction phasing method using a, three-wavelength data set collected at the Advanced Protein Source and, refined to a final R(work)/R(free) of 21.2 %/23.4 % with 33,271, independent reflections (Friedel pairs unmerged). The RNA duplex, crystallized in the tetragonal space group P4(1)22 with two independent, molecules in the asymmetric unit. The unit cell dimensions are a=b=47.18 A, and c=80.04 A. The helical region of the nonamer adopts the A-form, conformation. The uridine bulges assume similar conformations, with, uracils flipping out and protruding into the minor groove. The presence of, the bulge induces very large twist angles (approximately +50 degrees), between the base-pairs flanking the bulges while causing profound kinks in, the helix axis at the bulges. This severe twist and the large kink in turn, produces a very narrow major groove at the middle of the molecule. The, ribose sugars of the guanosines before the bulges adopt the C2'-endo, conformation while the rest, including the bulges, are in the C3'-endo, conformation. The intrastrand phosphate-phosphate (P-P) distance of the, phosphate groups flanking the bulges (approximately 4.4 A) are, significantly shorter than the average P-P distance in the duplex (6.0 A)., This short distance between the two phosphate groups brings the, non-bridging oxygen atoms close to each other where a calcium ion is bound, to each strand. The calcium ions in molecule 1 are well defined while the, calcium ions in molecule 2 are disordered.

About this Structure

1J9H is a Protein complex structure of sequences from [1] with CA as ligand. Full crystallographic information is available from OCA.

Reference

Crystal structure of an RNA duplex r(gugucgcac)(2) with uridine bulges., Xiong Y, Deng J, Sudarsanakumar C, Sundaralingam M, J Mol Biol. 2001 Oct 26;313(3):573-82. PMID:11676540

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