6o2l: Difference between revisions

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 ==NMR structure of the 2:1 complex of a carbazole derivative BMVC bound to c-MYC G-quadruplex==
-<StructureSection load='6o2l' size='340' side='right'caption='[[6o2l]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='6o2l' size='340' side='right'caption='[[6o2l]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6o2l]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O2L OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6O2L FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6o2l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O2L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6O2L FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BO6:3,6-bis[(E)-2-(1-methylpyridin-1-ium-4-yl)ethenyl]-9H-carbazole'>BO6</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=6o2l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o2l OCA], [http://pdbe.org/6o2l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o2l RCSB], [http://www.ebi.ac.uk/pdbsum/6o2l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o2l ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BO6:3,6-bis[(E)-2-(1-methylpyridin-1-ium-4-yl)ethenyl]-9H-carbazole'>BO6</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=6o2l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o2l OCA], [https://pdbe.org/6o2l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6o2l RCSB], [https://www.ebi.ac.uk/pdbsum/6o2l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6o2l ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-BMVC is the first fluorescent probe designed to detect G-quadruplexes (G4s) in vivo. The MYC oncogene promoter forms a G4 (MycG4) which acts as a transcription silencer. Here, we report the high-affinity and specific binding of BMVC to MycG4 with unusual slow-exchange rates on the NMR timescale. We also show that BMVC represses MYC in cancer cells. We determined the solution structures of the 1:1 and 2:1 BMVC-MycG4 complexes. BMVC first binds the 5'-end of MycG4 to form a 1:1 complex with a well-defined structure. At higher ratio, BMVC also binds the 3'-end to form a second complex. In both complexes, the crescent-shaped BMVC recruits a flanking DNA residue to form a BMVC-base plane stacking over the external G-tetrad. Remarkably, BMVC adjusts its conformation to a contracted form to match the G-tetrad for an optimal stacking interaction. This is the first structural example showing the importance of ligand conformational adjustment in G4 recognition. BMVC binds the more accessible 5'-end with higher affinity, whereas sequence specificity is present at the weaker-binding 3'-site. Our structures provide insights into specific recognition of MycG4 by BMVC and useful information for design of G4-targeted anticancer drugs and fluorescent probes.
-Structures of 1:1 and 2:1 complexes of BMVC and MYC promoter G-quadruplex reveal a mechanism of ligand conformation adjustment for G4-recognition.,Liu W, Lin C, Wu G, Dai J, Chang TC, Yang D Nucleic Acids Res. 2019 Dec 16;47(22):11931-11942. doi: 10.1093/nar/gkz1015. PMID:31740959<ref>PMID:31740959</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 6o2l" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Lin, C]]
+[[Category: Lin C]]
-[[Category: Liu, W]]
+[[Category: Liu W]]
-[[Category: Yang, D]]
+[[Category: Yang D]]
-[[Category: Bmvc]]
-[[Category: Dna]]
-[[Category: Drug-dna complex]]
-[[Category: G-quadruplex dna]]