1J9H

Crystal Structure of an RNA Duplex with Uridine Bulges

Summary for 1J9H

• Entry DOI: 10.2210/pdb1j9h/pdb
• Descriptor: 5'-R(*GP*UP*GP*UP*CP*GP*(CBR)P*AP*C)-3', CALCIUM ION (3 entities in total)
• Functional Keywords: uridine bulge, rna duplex, a-form, kink, metal binding, rna
• Total number of polymer chains: 4
• Total formula weight: 11802.87

Authors

Xiong, Y.,Deng, J.,Sudarsanakumar, C.,Sundaralingam, M. (deposition date: 2001-05-25, release date: 2001-10-26, Last modification date: 2024-02-07)

Primary citation

Xiong, Y.,Deng, J.,Sudarsanakumar, C.,Sundaralingam, M.
Crystal structure of an RNA duplex r(gugucgcac)(2) with uridine bulges.
J.Mol.Biol., 313:573-582, 2001

PubMed Abstract: 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.

PubMed: 11676540
DOI: 10.1006/jmbi.2001.5045

Experimental method

X-RAY DIFFRACTION (1.4 Å)