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409d

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[[Image:409d.gif|left|200px]]
 
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{{Structure
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==CRYSTAL STRUCTURE OF AN RNA R(CCCIUGGG) WITH THREE INDEPENDENT DUPLEXES INCORPORATING TANDEM I.U WOBBLES==
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|PDB= 409d |SIZE=350|CAPTION= <scene name='initialview01'>409d</scene>, resolution 2.50&Aring;
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<StructureSection load='409d' size='340' side='right'caption='[[409d]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=I:INOSINIC+ACID'>I</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
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<table><tr><td colspan='2'>[[409d]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=409D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=409D FirstGlance]. <br>
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|ACTIVITY=
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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]] 2.5&#8491;</td></tr>
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|GENE=
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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=409d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=409d OCA], [https://pdbe.org/409d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=409d RCSB], [https://www.ebi.ac.uk/pdbsum/409d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=409d ProSAT]</span></td></tr>
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|DOMAIN=
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</table>
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|RELATEDENTRY=
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__TOC__
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=409d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=409d OCA], [http://www.ebi.ac.uk/pdbsum/409d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=409d RCSB]</span>
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</StructureSection>
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}}
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[[Category: Large Structures]]
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[[Category: Hart D]]
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'''CRYSTAL STRUCTURE OF AN RNA R(CCCIUGGG) WITH THREE INDEPENDENT DUPLEXES INCORPORATING TANDEM I.U WOBBLES'''
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[[Category: Mitra SN]]
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[[Category: Pan B]]
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[[Category: Sun L]]
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==Overview==
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[[Category: Sundaralingam M]]
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The crystal structure of the RNA octamer duplex r(CCCIUGGG)2has been elucidated at 2.5 A resolution. The crystals belong to the space group P21and have unit cell constants a = 33.44 A, b = 43.41 A, c = 49.39 A and beta = 104.7 degrees with three independent duplexes (duplexes 1-3) in the asymmetric unit. The structure was solved by the molecular replacement method and refined to an Rwork/Rfree of 0.185/0.243 using 3765 reflections between 8.0 and 2.5 A. This is the first report of an RNA crystal structure incorporating I.U wobbles and three molecules in the asymmetric unit. Duplex 1 displays a kink of 24 degrees between the mismatch sites, while duplexes 2 and 3 have two kinks each of 19 degrees and 27 degrees, and 24 degrees and 29 degrees, respectively, on either side of the tandem mismatches. At the I.U/U.I mismatch steps, duplex 1 has a twist angle of 33.9 degrees, close to the average for all base pair steps, but duplexes 2 and 3 are underwound, with twist angles of 24.4 degrees and 26.5 degrees, respectively. The tandem I.U wobbles show intrastrand purine-pyrimidine stacking but exhibit interstrand purine-purine stacking with the flanking C.G pairs. The three independent duplexes are stacked non-coaxially in a head-to-tail fashion to form infinite pseudo-continuous helical columns which form intercolumn hydrogen bonding interactions through the 2'-hydroxyl groups where the minor grooves come together.
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==About this Structure==
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409D is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=409D OCA].
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==Reference==
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Crystal structure of an RNA octamer duplex r(CCCIUGGG)2 incorporating tandem I.U wobbles., Pan B, Mitra SN, Sun L, Hart D, Sundaralingam M, Nucleic Acids Res. 1998 Dec 15;26(24):5699-706. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9838002 9838002]
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[[Category: Protein complex]]
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[[Category: Hart, D.]]
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[[Category: Mitra, S N.]]
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[[Category: Pan, B.]]
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[[Category: Sun, L.]]
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[[Category: Sundaralingam, M.]]
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[[Category: double helix]]
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[[Category: i u wobble]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:36:52 2008''
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Current revision

CRYSTAL STRUCTURE OF AN RNA R(CCCIUGGG) WITH THREE INDEPENDENT DUPLEXES INCORPORATING TANDEM I.U WOBBLES

PDB ID 409d

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