5yze: Difference between revisions

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<StructureSection load='5yze' size='340' side='right'caption='[[5yze]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
<StructureSection load='5yze' size='340' side='right'caption='[[5yze]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5yze]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YZE FirstGlance]. <br>
<table><tr><td colspan='2'>[[5yze]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YZE FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=CPH:(1S)-5-DEOXY-1-O-METHYL-1-C-[(2R,3S)-3,5,7,10-TETRAHYDROXY-6-METHYL-4-OXO-1,2,3,4-TETRAHYDROANTHRACEN-2-YL]-D-XYLULOSE'>CPH</scene>, <scene name='pdbligand=1GL:4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE'>1GL</scene>, <scene name='pdbligand=ARI:[O4]-ACETOXY-2,3-DIDEOXYFUCOSE'>ARI</scene>, <scene name='pdbligand=CDR:2,3-DIDEOXYFUCOSE'>CDR</scene>, <scene name='pdbligand=ERI:4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-BETA-L-ARABINO-HEXOPYRANOSE'>ERI</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.87&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5yze FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yze OCA], [http://pdbe.org/5yze PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yze RCSB], [http://www.ebi.ac.uk/pdbsum/5yze PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yze ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1GL:4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE'>1GL</scene>, <scene name='pdbligand=ARI:[O4]-ACETOXY-2,3-DIDEOXYFUCOSE'>ARI</scene>, <scene name='pdbligand=CDR:2,3-DIDEOXYFUCOSE'>CDR</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=CPH:(1S)-5-DEOXY-1-O-METHYL-1-C-[(2R,3S)-3,5,7,10-TETRAHYDROXY-6-METHYL-4-OXO-1,2,3,4-TETRAHYDROANTHRACEN-2-YL]-D-XYLULOSE'>CPH</scene>, <scene name='pdbligand=ERI:4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-BETA-L-ARABINO-HEXOPYRANOSE'>ERI</scene></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=5yze FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yze OCA], [https://pdbe.org/5yze PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yze RCSB], [https://www.ebi.ac.uk/pdbsum/5yze PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yze ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We have reported the propensity of a DNA sequence containing CCG repeats to form a stable i-motif tetraplex structure in the absence of ligands. Here we show that an i-motif DNA sequence may transition to a base-extruded duplex structure with a GGCC tetranucleotide tract when bound to the (Co(II))-mediated dimer of chromomycin A3, Co(II)(Chro)(2). Biophysical experiments reveal that CCG trinucleotide repeats provide favorable binding sites for Co(II)(Chro)(2). In addition, water hydration and divalent metal ion (Co(II)) interactions also play a crucial role in the stabilization of CCG trinucleotide repeats (TNRs). Our data furnish useful structural information for the design of novel therapeutic strategies to treat neurological diseases caused by repeat expansions.
Co(II)(Chromomycin)(2) Complex Induces a Conformational Change of CCG Repeats from i-Motif to Base-Extruded DNA Duplex.,Chen YW, Satange R, Wu PC, Jhan CR, Chang CK, Chung KR, Waring MJ, Lin SW, Hsieh LC, Hou MH Int J Mol Sci. 2018 Sep 17;19(9). pii: ijms19092796. doi: 10.3390/ijms19092796. PMID:30227633<ref>PMID:30227633</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5yze" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Chen, Y W]]
[[Category: Synthetic construct]]
[[Category: Hou, M H]]
[[Category: Chen YW]]
[[Category: Satange, R B]]
[[Category: Hou MH]]
[[Category: Wu, P C]]
[[Category: Satange RB]]
[[Category: Antibiotics-dna complex]]
[[Category: Wu PC]]
[[Category: Ccg repeat]]
[[Category: Chromomycin a3]]
[[Category: Dna]]
[[Category: Drug-dna complex]]
[[Category: Flipout]]
[[Category: I-motif]]
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