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| [[Image:1efo.gif|left|200px]]<br /><applet load="1efo" size="450" color="white" frame="true" align="right" spinBox="true"
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| caption="1efo, resolution 2.30Å" />
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| '''CRYSTAL STRUCTURE OF AN ADENINE BULGE IN THE RNA CHAIN OF A DNA/RNA HYBRID, D(CTCCTCTTC)/R(GAAGAGAGAG)'''<br />
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| ==Overview== | | ==CRYSTAL STRUCTURE OF AN ADENINE BULGE IN THE RNA CHAIN OF A DNA/RNA HYBRID, D(CTCCTCTTC)/R(GAAGAGAGAG)== |
| 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.
| | <StructureSection load='1efo' size='340' side='right'caption='[[1efo]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | | == Structural highlights == |
| ==About this Structure== | | <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> |
| 1EFO is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EFO OCA].
| | </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> |
| ==Reference== | | </table> |
| 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://ispc.weizmann.ac.il//pmbin/getpm?pmid=10860725 10860725]
| | __TOC__ |
| [[Category: Protein complex]]
| | </StructureSection> |
| [[Category: Sudarsanakumar, C.]] | | [[Category: Large Structures]] |
| [[Category: Sundaralingam, M.]]
| | [[Category: Sudarsanakumar C]] |
| [[Category: Xiong, Y.]]
| | [[Category: Sundaralingam M]] |
| [[Category: a-form conformation]]
| | [[Category: Xiong Y]] |
| [[Category: adenine bulge]] | |
| [[Category: hybrid]] | |
| [[Category: looped out]] | |
| [[Category: x-ray structure]] | |
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| ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:10:32 2007''
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