OCA at 15:52, 27 October 2021

OCA — Wed, 27 Oct 2021 15:52:14 GMT

←Older revision		Revision as of 15:52, 27 October 2021
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	==Solution Structure of Berberine Bound to a dGMP Fill-in G-Quadruplex in the PDGFR-b Promoter==		==Solution Structure of Berberine Bound to a dGMP Fill-in G-Quadruplex in the PDGFR-b Promoter==
-	<StructureSection load='7msv' size='340' side='right'caption='[[7msv]]' scene=''>	+	<StructureSection load='7msv' size='340' side='right'caption='[[7msv]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' 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=7MSV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MSV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7msv]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MSV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MSV FirstGlance]. <br>
-	</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=7msv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7msv OCA], [https://pdbe.org/7msv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7msv RCSB], [https://www.ebi.ac.uk/pdbsum/7msv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7msv 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=BER:BERBERINE'>BER</scene>, <scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</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=7msv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7msv OCA], [https://pdbe.org/7msv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7msv RCSB], [https://www.ebi.ac.uk/pdbsum/7msv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7msv ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The G-quadruplexes (G4s) formed in the PDGFR-beta gene promoter are transcriptional modulators and amenable to small-molecule targeting. Berberine (BER), a clinically important natural isoquinoline alkaloid, has gained increasing attention due to its potential as anticancer drug. We previously showed that the PDGFR-beta gene promoter forms a unique vacancy G4 (vG4) that can be filled in and stabilized by guanine metabolites, such as dGMP. Herein, we report the high-resolution NMR structure of a ternary complex of berberine bound to the dGMP-fill-in PDGFR-beta vG4 in potassium solution. This is the first small-molecule complex structure of a fill-in vG4. This ternary complex has a 2:1:1 binding stoichiometry with a berberine molecule bound at each the 5'- and 3'-end of the 5'-dGMP-fill-in PDGFR-beta vG4. Each berberine recruits the adjacent adenine residue from the 5'- or 3'-flanking sequence to form a "quasi-triad plane" that covers the external G-tetrad of the fill-in vG4, respectively. Significantly, berberine covers and stabilizes the fill-in dGMP. The binding of berberine involves both pi-stacking and electrostatic interactions, and the fill-in dGMP is covered and well-protected by berberine. The NMR structure can guide rational design of berberine analogues that target the PDGFR-beta vG4 or dGMP-fill-in vG4. Moreover, our structure provides a molecular basis for designing small-molecule guanine conjugates to target vG4s.
		+
		+	Solution Structure of Ternary Complex of Berberine Bound to a dGMP-Fill-In Vacancy G-Quadruplex Formed in the PDGFR-beta Promoter.,Wang KB, Dickerhoff J, Yang D J Am Chem Soc. 2021 Oct 13;143(40):16549-16555. doi: 10.1021/jacs.1c06200. Epub, 2021 Sep 29. PMID:34586799<ref>PMID:34586799</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7msv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dickerhoff J]]	+	[[Category: Dickerhoff, J]]
-	[[Category: Wang KB]]	+	[[Category: Wang, K B]]
-	[[Category: Yang D]]	+	[[Category: Yang, D]]
		+	[[Category: Dna]]
		+	[[Category: G-quadruplex]]
		+	[[Category: Guanine metabolite]]
		+	[[Category: Promoter]]

OCA at 16:29, 20 October 2021

OCA — Wed, 20 Oct 2021 16:29:44 GMT

←Older revision		Revision as of 16:29, 20 October 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7msv is ~~ON HOLD until Paper Publication~~	+	==Solution Structure of Berberine Bound to a dGMP Fill-in G-Quadruplex in the PDGFR-b Promoter==
-		+	<StructureSection load='7msv' size='340' side='right'caption='[[7msv]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MSV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MSV FirstGlance]. <br>
-	~~Description~~:	+	</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=7msv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7msv OCA], [https://pdbe.org/7msv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7msv RCSB], [https://www.ebi.ac.uk/pdbsum/7msv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7msv ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Dickerhoff J]]
		+	[[Category: Wang KB]]
		+	[[Category: Yang D]]

OCA at 11:05, 9 June 2021

OCA — Wed, 09 Jun 2021 11:05:49 GMT

←Older revision		Revision as of 11:05, 9 June 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7msv is ON HOLD	+	The entry 7msv is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7msv" [edit=sysop:move=sysop]

OCA — Wed, 19 May 2021 08:58:06 GMT

Protected "7msv" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:58, 19 May 2021

OCA: New page: '''Unreleased structure''' The entry 7msv is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 19 May 2021 08:58:05 GMT

New page: '''Unreleased structure''' The entry 7msv is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7msv is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7msv - Revision history

OCA at 15:52, 27 October 2021

OCA at 16:29, 20 October 2021

OCA at 11:05, 9 June 2021

OCA: Protected "7msv" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7msv is ON HOLD Authors: Description: Category: Unreleased Structures