From Proteopedia
(Difference between revisions)
proteopedia linkproteopedia link
|
|
| Line 1: |
Line 1: |
| - | [[Image:1j9h.gif|left|200px]] | + | {{Seed}} |
| | + | [[Image:1j9h.png|left|200px]] |
| | | | |
| | <!-- | | <!-- |
| Line 9: |
Line 10: |
| | {{STRUCTURE_1j9h| PDB=1j9h | SCENE= }} | | {{STRUCTURE_1j9h| PDB=1j9h | SCENE= }} |
| | | | |
| - | '''Crystal Structure of an RNA Duplex with Uridine Bulges'''
| + | ===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. | + | The line below this paragraph, {{ABSTRACT_PUBMED_11676540}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 11676540 is the PubMed ID number. |
| | + | --> |
| | + | {{ABSTRACT_PUBMED_11676540}} |
| | | | |
| | ==About this Structure== | | ==About this Structure== |
| Line 29: |
Line 33: |
| | [[Category: Rna duplex]] | | [[Category: Rna duplex]] |
| | [[Category: Uridine bulge]] | | [[Category: Uridine bulge]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 20:56:51 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 14:42:50 2008'' |
Revision as of 11:42, 1 July 2008
Template:STRUCTURE 1j9h
Crystal Structure of an RNA Duplex with Uridine Bulges
Template:ABSTRACT PUBMED 11676540
About this Structure
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 Tue Jul 1 14:42:50 2008
