6pnk - Revision history

OCA at 07:32, 11 October 2023

OCA — Wed, 11 Oct 2023 07:32:22 GMT

←Older revision		Revision as of 07:32, 11 October 2023
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	<StructureSection load='6pnk' size='340' side='right'caption='[[6pnk]], [[Resolution\|resolution]] 2.39Å' scene=''>		<StructureSection load='6pnk' size='340' side='right'caption='[[6pnk]], [[Resolution\|resolution]] 2.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pnk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PNK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6PNK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pnk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Tetrahymena_thermophila Tetrahymena thermophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PNK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PNK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MMP:N-METHYLMESOPORPHYRIN'>MMP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.39Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6p45\|6p45]]</div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MMP:N-METHYLMESOPORPHYRIN'>MMP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=6pnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pnk OCA], [~~http~~://pdbe.org/6pnk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pnk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pnk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pnk ProSAT]</span></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=6pnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pnk OCA], [https://pdbe.org/6pnk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pnk RCSB], [https://www.ebi.ac.uk/pdbsum/6pnk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pnk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lin, L Y~~]]	+	[[Category: Tetrahymena thermophila]]
-	[[Category: ~~Yatsunyk, L A~~]]	+	[[Category: Lin LY]]
-	[[Category: ~~Dna]]~~	+	[[Category: Yatsunyk LA]]
-	~~[[Category: End-stacking]]~~	+
-	~~[[Category: Parallel g-quadruplex]]~~	+
-	~~[[Category: Tt propeller loop~~]]	+

OCA at 07:06, 25 November 2020

OCA — Wed, 25 Nov 2020 07:06:17 GMT

←Older revision		Revision as of 07:06, 25 November 2020
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	==Crystal structure of the G-quadruplex formed by (GGGTT)3GGG in complex with N-methylmesoporphryin IX==		==Crystal structure of the G-quadruplex formed by (GGGTT)3GGG in complex with N-methylmesoporphryin IX==
-	<StructureSection load='6pnk' size='340' side='right'caption='[[6pnk]]' scene=''>	+	<StructureSection load='6pnk' size='340' side='right'caption='[[6pnk]], [[Resolution\|resolution]] 2.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PNK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PNK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pnk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PNK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PNK FirstGlance]. <br>
-	</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=6pnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pnk OCA], [http://pdbe.org/6pnk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pnk RCSB], [http://www.ebi.ac.uk/pdbsum/6pnk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pnk ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MMP:N-METHYLMESOPORPHYRIN'>MMP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6p45\|6p45]]</div></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=6pnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pnk OCA], [http://pdbe.org/6pnk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pnk RCSB], [http://www.ebi.ac.uk/pdbsum/6pnk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pnk ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The G-quadruplex (GQ) is a well-studied non-canonical DNA structure formed by G-rich sequences found at telomeres and gene promoters. Biological studies suggest that GQs may play roles in regulating gene expression, DNA replication, and DNA repair. Small molecule ligands were shown to alter GQ structure and stability and thereby serve as novel therapies, particularly against cancer. In this work, we investigate the interaction of a G-rich sequence, 5'-GGGTTGGGTTGGGTTGGG-3' (T1), with a water-soluble porphyrin, N-methyl mesoporphyrin IX (NMM) via biophysical and X-ray crystallographic studies. UV-vis and fluorescence titrations, as well as a Job plot, revealed a 1:1 binding stoichiometry with an impressively tight binding constant of 30-50 muM-1 and DeltaG298 of -10.3 kcal/mol. Eight extended variants of T1 (named T2 -T9) were fully characterized and T7 was identified as a suitable candidate for crystallographic studies. We solved the crystal structures of the T1- and T7-NMM complexes at 2.39 and 2.34 A resolution, respectively. Both complexes form a 5'-5' dimer of parallel GQs capped by NMM at the 3' G-quartet, supporting the 1:1 binding stoichiometry. Our work provides invaluable details about GQ-ligand binding interactions and informs the design of novel anticancer drugs that selectively recognize specific GQs and modulate their stability for therapeutic purposes.
		+
		+	Biophysical and X-ray structural studies of the (GGGTT)3GGG G-quadruplex in complex with N-methyl mesoporphyrin IX.,Lin LY, McCarthy S, Powell BM, Manurung Y, Xiang IM, Dean WL, Chaires B, Yatsunyk LA PLoS One. 2020 Nov 18;15(11):e0241513. doi: 10.1371/journal.pone.0241513., eCollection 2020. PMID:33206666<ref>PMID:33206666</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6pnk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lin LY]]	+	[[Category: Lin, L Y]]
-	[[Category: Yatsunyk LA]]	+	[[Category: Yatsunyk, L A]]
		+	[[Category: Dna]]
		+	[[Category: End-stacking]]
		+	[[Category: Parallel g-quadruplex]]
		+	[[Category: Tt propeller loop]]

OCA at 14:01, 8 July 2020

OCA — Wed, 08 Jul 2020 14:01:19 GMT

←Older revision		Revision as of 14:01, 8 July 2020
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-	'''Unreleased structure'''

-	~~The entry 6pnk is ON HOLD until Paper Publication~~	+	==Crystal structure of the G-quadruplex formed by (GGGTT)3GGG in complex with N-methylmesoporphryin IX==
-		+	<StructureSection load='6pnk' size='340' side='right'caption='[[6pnk]]' scene=''>
-	~~Authors: Yatsunyk, L.A., Lin, L.Y.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PNK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PNK FirstGlance]. <br>
-	~~Description:~~ Crystal structure of the G-quadruplex formed by (GGGTT)3GGG in complex with N-methylmesoporphryin IX	+	</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=6pnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pnk OCA], [http://pdbe.org/6pnk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pnk RCSB], [http://www.ebi.ac.uk/pdbsum/6pnk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pnk ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Lin~~, L.Y~~]]	+	__TOC__
-	[[Category: Yatsunyk~~, L.A~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lin LY]]
		+	[[Category: Yatsunyk LA]]

OCA at 04:15, 7 August 2019

OCA — Wed, 07 Aug 2019 04:15:27 GMT

←Older revision		Revision as of 04:15, 7 August 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6pnk is ON HOLD	+	The entry 6pnk is ON HOLD until Paper Publication

	Authors: Yatsunyk, L.A., Lin, L.Y.		Authors: Yatsunyk, L.A., Lin, L.Y.

OCA: Protected "6pnk" [edit=sysop:move=sysop]

OCA — Wed, 10 Jul 2019 04:18:27 GMT

Protected "6pnk" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:18, 10 July 2019

OCA: New page: '''Unreleased structure''' The entry 6pnk is ON HOLD Authors: Yatsunyk, L.A., Lin, L.Y. Description: Crystal structure of the G-quadruplex formed by (GGGTT)3GGG in complex with N-methy...

OCA — Wed, 10 Jul 2019 04:18:26 GMT

New page: '''Unreleased structure''' The entry 6pnk is ON HOLD Authors: Yatsunyk, L.A., Lin, L.Y. Description: Crystal structure of the G-quadruplex formed by (GGGTT)3GGG in complex with N-methy...

New page

'''Unreleased structure'''

The entry 6pnk is ON HOLD

Authors: Yatsunyk, L.A., Lin, L.Y.

Description: Crystal structure of the G-quadruplex formed by (GGGTT)3GGG in complex with N-methylmesoporphryin IX
[[Category: Unreleased Structures]]
[[Category: Lin, L.Y]]
[[Category: Yatsunyk, L.A]]