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| | ==Crystal Structure of an RNA Duplex with Uridine Bulges== | | ==Crystal Structure of an RNA Duplex with Uridine Bulges== |
| - | <StructureSection load='1j9h' size='340' side='right' caption='[[1j9h]], [[Resolution|resolution]] 1.40Å' scene=''> | + | <StructureSection load='1j9h' size='340' side='right'caption='[[1j9h]], [[Resolution|resolution]] 1.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1j9h]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J9H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J9H FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1j9h]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J9H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J9H FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4Å</td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene></td></tr> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1j9h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j9h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j9h RCSB], [http://www.ebi.ac.uk/pdbsum/1j9h PDBsum]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1j9h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j9h OCA], [https://pdbe.org/1j9h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j9h RCSB], [https://www.ebi.ac.uk/pdbsum/1j9h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j9h ProSAT]</span></td></tr> |
| - | <table>
| + | </table> |
| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | 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.
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| - | 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<ref>PMID:11676540</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div> | + | |
| - | == References ==
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| - | <references/> | + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Deng, J.]] | + | [[Category: Large Structures]] |
| - | [[Category: Sudarsanakumar, C.]] | + | [[Category: Deng J]] |
| - | [[Category: Sundaralingam, M.]] | + | [[Category: Sudarsanakumar C]] |
| - | [[Category: Xiong, Y.]] | + | [[Category: Sundaralingam M]] |
| - | [[Category: A-form]]
| + | [[Category: Xiong Y]] |
| - | [[Category: Kink]]
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| - | [[Category: Metal binding]]
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| - | [[Category: Rna]]
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| - | [[Category: Rna duplex]]
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| - | [[Category: Uridine bulge]]
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