1j9h
From Proteopedia
(New page: 200px<br /><applet load="1j9h" size="450" color="white" frame="true" align="right" spinBox="true" caption="1j9h, resolution 1.4Å" /> '''Crystal Structure of ...) |
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| - | [[Image:1j9h.gif|left|200px]]<br /><applet load="1j9h" size=" | + | [[Image:1j9h.gif|left|200px]]<br /><applet load="1j9h" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1j9h, resolution 1.4Å" /> | caption="1j9h, resolution 1.4Å" /> | ||
'''Crystal Structure of an RNA Duplex with Uridine Bulges'''<br /> | '''Crystal Structure of an RNA Duplex with Uridine Bulges'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of a nonamer RNA duplex with a uridine bulge in each | + | 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== | ==About this Structure== | ||
| - | 1J9H is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1J9H is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J9H OCA]. |
==Reference== | ==Reference== | ||
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[[Category: uridine bulge]] | [[Category: uridine bulge]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:20:09 2008'' |
Revision as of 11:20, 21 February 2008
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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 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
Page seeded by OCA on Thu Feb 21 13:20:09 2008
Categories: Protein complex | Deng, J. | Sudarsanakumar, C. | Sundaralingam, M. | Xiong, Y. | CA | A-form | Kink | Metal binding | Rna duplex | Uridine bulge
