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| <!--
| | ==CRYSTAL STRUCTURE OF AN ADENINE BULGE IN THE RNA CHAIN OF A DNA/RNA HYBRID, D(CTCCTCTTC)/R(GAAGAGAGAG)== |
| The line below this paragraph, containing "STRUCTURE_1efo", creates the "Structure Box" on the page.
| | <StructureSection load='1efo' size='340' side='right'caption='[[1efo]], [[Resolution|resolution]] 2.30Å' scene=''> |
| You may change the PDB parameter (which sets the PDB file loaded into the applet)
| | == Structural highlights == |
| or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| | <table><tr><td colspan='2'>[[1efo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EFO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EFO FirstGlance]. <br> |
| or leave the SCENE parameter empty for the default display.
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</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=1efo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1efo OCA], [https://pdbe.org/1efo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1efo RCSB], [https://www.ebi.ac.uk/pdbsum/1efo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1efo ProSAT]</span></td></tr> |
| {{STRUCTURE_1efo| PDB=1efo | SCENE= }}
| | </table> |
| | | __TOC__ |
| '''CRYSTAL STRUCTURE OF AN ADENINE BULGE IN THE RNA CHAIN OF A DNA/RNA HYBRID, D(CTCCTCTTC)/R(GAAGAGAGAG)'''
| | </StructureSection> |
| | | [[Category: Large Structures]] |
| | | [[Category: Sudarsanakumar C]] |
| ==Overview==
| | [[Category: Sundaralingam M]] |
| Crystal structure of a DNA.RNA hybrid, d(CTCCTCTTC).r(gaagagagag), with an adenine bulge in the polypurine RNA strand was determined at 2.3 A resolution. The structure was solved by the molecular replacement method and refined to a final R-factor of 19.9% (Rfree 22.2%). The hybrid duplex crystallized in the space group I222 with unit cell dimensions, a = 46.66 A, b = 47.61 A and c = 54.05 A, and adopts the A-form conformation. All RNA and DNA sugars are in the C3'-endo conformation, the glycosyl angles in anti conformation and the majority of the C4'-C5' torsion angles in g+ except two trans angles, in conformity with the C3'-endo rigid nucleotide hypothesis. The adenine bulge is looped out and it is also in the anti C3'-endo conformation. The bulge is involved in a base-triple (C.g)*a interaction with the end base-pair (C9.g10) in the minor groove of a symmetry-related molecule. The 2' hydroxyl group of g15 is hydrogen bonded to O2P and O5' of g17, skipping the bulged adenine a16 and stabilizing the sugar-phosphate backbone of the hybrid. The hydrogen bonding and the backbone conformation at the bulged adenine site is very similar to that found in the crystal structure of a protein-RNA complex.
| | [[Category: Xiong Y]] |
| | |
| ==About this Structure== | |
| Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EFO OCA]. | |
| | |
| ==Reference== | |
| Crystal structure of an adenine bulge in the RNA chain of a DNA.RNA hybrid, d(CTCCTCTTC).r(gaagagagag)., Sudarsanakumar C, Xiong Y, Sundaralingam M, J Mol Biol. 2000 May 26;299(1):103-12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10860725 10860725]
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| [[Category: Sudarsanakumar, C.]]
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| [[Category: Sundaralingam, M.]]
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| [[Category: Xiong, Y.]] | |
| [[Category: A-form conformation]]
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| [[Category: Adenine bulge]] | |
| [[Category: Hybrid]] | |
| [[Category: Looped out]] | |
| [[Category: X-ray structure]] | |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 15:02:20 2008''
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