1v3p

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[[Image:1v3p.gif|left|200px]]
 
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==Crystal structure of d(GCGAGAGC): the DNA octaplex structure with I-motif of G-quartet==
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The line below this paragraph, containing "STRUCTURE_1v3p", creates the "Structure Box" on the page.
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<StructureSection load='1v3p' size='340' side='right'caption='[[1v3p]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1v3p]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V3P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V3P FirstGlance]. <br>
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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]] 2.3&#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=C38:5-IODO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C38</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
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{{STRUCTURE_1v3p| PDB=1v3p | SCENE= }}
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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=1v3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v3p OCA], [https://pdbe.org/1v3p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v3p RCSB], [https://www.ebi.ac.uk/pdbsum/1v3p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v3p ProSAT]</span></td></tr>
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</table>
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'''Crystal structure of d(GCGAGAGC): the DNA octaplex structure with I-motif of G-quartet'''
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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==Overview==
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Recent genomic analyses revealed many kinds of tandem repeats of specific sequences. Some of them are related to genetic diseases, but their biological functions and structures are still unknown. Two X-ray structures of a short DNA fragment d(gcGA[G]1Agc) show that four base-intercalated duplexes are assembled to form an octaplex at a low K+ concentration, in which the eight G5 residues form a stacked double G-quartet in the central part. At a higher K+ concentration, however, the octaplex is split into just two halves. These structural features suggest a folding process of eight tandem repeats of d(ccGA[G]4Agg), according to a double Greek-key motif. Such a packaging of the repeats could facilitate slippage of a certain sequence during DNA replication, to induce increase or decrease of the repeats.
Recent genomic analyses revealed many kinds of tandem repeats of specific sequences. Some of them are related to genetic diseases, but their biological functions and structures are still unknown. Two X-ray structures of a short DNA fragment d(gcGA[G]1Agc) show that four base-intercalated duplexes are assembled to form an octaplex at a low K+ concentration, in which the eight G5 residues form a stacked double G-quartet in the central part. At a higher K+ concentration, however, the octaplex is split into just two halves. These structural features suggest a folding process of eight tandem repeats of d(ccGA[G]4Agg), according to a double Greek-key motif. Such a packaging of the repeats could facilitate slippage of a certain sequence during DNA replication, to induce increase or decrease of the repeats.
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==About this Structure==
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Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats.,Kondo J, Adachi W, Umeda S, Sunami T, Takenaka A Nucleic Acids Res. 2004 May 7;32(8):2541-9. Print 2004. PMID:15133122<ref>PMID:15133122</ref>
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V3P OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats., Kondo J, Adachi W, Umeda S, Sunami T, Takenaka A, Nucleic Acids Res. 2004 May 7;32(8):2541-9. Print 2004. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15133122 15133122]
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</div>
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[[Category: Kondo, J.]]
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<div class="pdbe-citations 1v3p" style="background-color:#fffaf0;"></div>
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[[Category: Sunami, T.]]
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== References ==
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[[Category: Takenaka, A.]]
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<references/>
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[[Category: Umeda, S.]]
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__TOC__
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[[Category: Base-intercalated duplex]]
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</StructureSection>
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[[Category: Base-intercalated motif]]
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[[Category: Large Structures]]
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[[Category: Crystal structure]]
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[[Category: Kondo J]]
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[[Category: Deoxyribonucleic acid]]
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[[Category: Sunami T]]
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[[Category: Dna]]
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[[Category: Takenaka A]]
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[[Category: G-quartet]]
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[[Category: Umeda S]]
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[[Category: I-motif]]
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[[Category: I-motif of g-quartet]]
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[[Category: Octaplex]]
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[[Category: Quadruplex]]
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[[Category: Sheared g:a pair]]
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[[Category: X-ray analysis]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 12:02:14 2008''
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Current revision

Crystal structure of d(GCGAGAGC): the DNA octaplex structure with I-motif of G-quartet

PDB ID 1v3p

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