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1fuf

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[[Image:1fuf.gif|left|200px]]<br /><applet load="1fuf" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1fuf, resolution 1.7&Aring;" />
 
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'''CRYSTAL STRUCTURE OF A 14BP RNA OLIGONUCLEOTIDE CONTAINING DOUBLE UU BULGES: A NOVEL INTRAMOLECULAR U*(AU) BASE TRIPLE'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF A 14BP RNA OLIGONUCLEOTIDE CONTAINING DOUBLE UU BULGES: A NOVEL INTRAMOLECULAR U*(AU) BASE TRIPLE==
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The RNA/DNA 14-mer, (gguauuucgguaCc)2 with consecutive uridine bulges (underlined) on each strand has been determined in two crystal forms, spermine bound (Sp-form) and spermine free (Sp-free). The former was solved by the MAD method with three-wavelength data collected at Brookhaven National Laboratory (BNL); the later isomorphous structure was solved by the molecular replacement method using data collected on our Raxis IIc imaging plate system. The two crystal forms belong to the space group C2 with one molecule of double-stranded 14 mer in the asymmetric unit. The Sp-form has cell constants, a = 60.06, b = 29.10, c = 52.57 A, beta = 120.79 degrees and was refined to 1.7 A resolution with a final Rwork/Rfree of 19.8%/22.7% using 8,549 independent reflections. The Sp-free structure has cell constants, a = 60.06, b = 29.58, c = 52.50 A, beta = 120.85 degrees and was refined to 1.8 A with a final Rwork/ Rfree of 20.8%/23.2% using 6,285 unique reflections. The two structures are identical, except that the Sp-form has a spermine bound in the major groove, parallel to the RNA helical axis. One of the uridine bulges forms a novel intramolecular U*(A x U) base triple. The helices are in the C3'-endo conformation (A-form), but the bulges adopt the C2'-endo sugar pucker. Furthermore, the bulges induce a kink (30 degrees) in the helix axis and a very large twist (55 degrees) between the base pairs flanking the bulges. The Sp-form has one Mg2+ ion whereas the Sp-free form has two Mg2+ ions.
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<StructureSection load='1fuf' size='340' side='right'caption='[[1fuf]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1fuf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FUF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FUF FirstGlance]. <br>
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1FUF is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=SPM:'>SPM</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FUF OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fuf OCA], [https://pdbe.org/1fuf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fuf RCSB], [https://www.ebi.ac.uk/pdbsum/1fuf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fuf ProSAT]</span></td></tr>
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Crystal structures of two forms of a 14-mer RNA/DNA chimer duplex with double UU bulges: a novel intramolecular U*(A x U) base triple., Deng J, Xiong Y, Sudarsanakumar C, Shi K, Sundaralingam M, RNA. 2001 Oct;7(10):1425-31. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11680847 11680847]
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</table>
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[[Category: Protein complex]]
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__TOC__
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[[Category: Deng, J.]]
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</StructureSection>
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[[Category: Shi, K.]]
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[[Category: Large Structures]]
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[[Category: Sudarsanakumar, C.]]
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[[Category: Deng J]]
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[[Category: Sundaralingam, M.]]
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[[Category: Shi K]]
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[[Category: Xiong, Y.]]
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[[Category: Sudarsanakumar C]]
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[[Category: MG]]
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[[Category: Sundaralingam M]]
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[[Category: SPM]]
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[[Category: Xiong Y]]
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[[Category: base triple]]
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[[Category: bulge]]
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[[Category: crystal]]
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[[Category: rna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:42:45 2008''
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Current revision

CRYSTAL STRUCTURE OF A 14BP RNA OLIGONUCLEOTIDE CONTAINING DOUBLE UU BULGES: A NOVEL INTRAMOLECULAR U*(AU) BASE TRIPLE

PDB ID 1fuf

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