7djv - Revision history

OCA: Replacing page with 'REMOVED: The PDB entry 7djv was removed.'

2024-04-03T05:45:33Z

Replacing page with 'REMOVED: The PDB entry 7djv was removed.'

←Older revision		Revision as of 05:45, 3 April 2024
Line 1:		Line 1:
-		+	REMOVED: The PDB entry 7djv was removed.
-	~~==NMR solution structure of the 2~~:~~1 complex of a platinum(II) compound bound to Myc1234 G-quadruplex reveals the mechanism of conformational switch and dynamic binding of G-quadruplex==~~	+
-	~~<StructureSection load='~~7djv~~' size='340' side='right'caption='[[7djv]]' scene=''>~~	+
-	~~== Structural highlights ==~~	+
-	~~<table><tr><td colspan='2'>[[7djv]] 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=7DJV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DJV FirstGlance]. <br>	+
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=H9C:Bis(1,10-phenanthroline)platinum(II)'>H9C</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=7djv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7djv OCA], [https://pdbe.org/7djv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7djv RCSB], [https://www.ebi.ac.uk/pdbsum/7djv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7djv ProSAT]</span></td></tr>	+
-	~~</table>~~	+
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	G-quadruplex (G4) transitions play integral roles in regulating biological functions and can be modified by ligands. However, little is known about G4 transitions. Herein, we reveal distinct pathways of a platinum(II) compound Pt-phen converting parallel-stranded MYC G4 to a hybrid-type structure. Three NMR structures, 1:1 5'-end binding, 1:1 3'-end binding and 2:1 Pt-phen-MYC G4 complexes, were determined by NMR. We find that Pt-phen drives G4 transition at a low ratio. Under physiological 100 mM K+ conditions, a significant stable hydrogen-bonded T:T:A triad is formed at 3'-end of hybrid-type Myc1234, and consequently, Pt-phen first binds the 5'-end to form a 1:1 5'-end binding complex and then disrupts the 3' T:T:A triad and binds 3'-end to form a 2:1 complex with more Pt-phen. Remarkably, the G4 transition pathway is different in 5 mM K+ with Pt-phen first binding the 3'-end and then the 5'-end. 'Edgewise-loop and flanking/ligand/G-tetrad' sandwich structure formation and terminal T:T:A triad stabilization play decisive roles in advancing and altering transition pathways. Our work is the first to elucidate the molecular structures of G4 transitions driven by a small molecule. The ligand-driven G4 transition is a dynamic process that includes a quick G4 transition and multiple complexes formation.	+
-		+
-	G-quadruplex structural transition driven by a platinum compound.,Liu W, Zhu BC, Liu LY, Xia XY, Mao ZW Nucleic Acids Res. 2022 Aug 12;50(14):7816-7828. doi: 10.1093/nar/gkac572. PMID:35766415<ref>PMID:35766415</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 7djv" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
-	~~__TOC__~~	+
-	~~</StructureSection>~~	+
-	~~[[Category: Homo sapiens]]~~	+
-	~~[[Category: Large Structures]]~~	+
-	~~[[Category: Liu W]]~~	+
-	~~[[Category: Mao ZW]]~~	+

OCA at 10:06, 21 December 2022

2022-12-21T10:06:22Z

←Older revision		Revision as of 10:06, 21 December 2022
Line 3:		Line 3:
	<StructureSection load='7djv' size='340' side='right'caption='[[7djv]]' scene=''>		<StructureSection load='7djv' size='340' side='right'caption='[[7djv]]' 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=7DJV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DJV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7djv]] 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=7DJV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DJV 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=7djv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7djv OCA], [https://pdbe.org/7djv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7djv RCSB], [https://www.ebi.ac.uk/pdbsum/7djv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7djv 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=H9C:Bis(1,10-phenanthroline)platinum(II)'>H9C</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=7djv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7djv OCA], [https://pdbe.org/7djv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7djv RCSB], [https://www.ebi.ac.uk/pdbsum/7djv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7djv ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	G-quadruplex (G4) transitions play integral roles in regulating biological functions and can be modified by ligands. However, little is known about G4 transitions. Herein, we reveal distinct pathways of a platinum(II) compound Pt-phen converting parallel-stranded MYC G4 to a hybrid-type structure. Three NMR structures, 1:1 5'-end binding, 1:1 3'-end binding and 2:1 Pt-phen-MYC G4 complexes, were determined by NMR. We find that Pt-phen drives G4 transition at a low ratio. Under physiological 100 mM K+ conditions, a significant stable hydrogen-bonded T:T:A triad is formed at 3'-end of hybrid-type Myc1234, and consequently, Pt-phen first binds the 5'-end to form a 1:1 5'-end binding complex and then disrupts the 3' T:T:A triad and binds 3'-end to form a 2:1 complex with more Pt-phen. Remarkably, the G4 transition pathway is different in 5 mM K+ with Pt-phen first binding the 3'-end and then the 5'-end. 'Edgewise-loop and flanking/ligand/G-tetrad' sandwich structure formation and terminal T:T:A triad stabilization play decisive roles in advancing and altering transition pathways. Our work is the first to elucidate the molecular structures of G4 transitions driven by a small molecule. The ligand-driven G4 transition is a dynamic process that includes a quick G4 transition and multiple complexes formation.
		+
		+	G-quadruplex structural transition driven by a platinum compound.,Liu W, Zhu BC, Liu LY, Xia XY, Mao ZW Nucleic Acids Res. 2022 Aug 12;50(14):7816-7828. doi: 10.1093/nar/gkac572. PMID:35766415<ref>PMID:35766415</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7djv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Liu W]]		[[Category: Liu W]]
	[[Category: Mao ZW]]		[[Category: Mao ZW]]

OCA at 09:55, 12 January 2022

2022-01-12T09:55:43Z

←Older revision		Revision as of 09:55, 12 January 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7djv is ON HOLD until Paper Publication~~	+	==NMR solution structure of the 2:1 complex of a platinum(II) compound bound to Myc1234 G-quadruplex reveals the mechanism of conformational switch and dynamic binding of G-quadruplex==
-		+	<StructureSection load='7djv' size='340' side='right'caption='[[7djv]]' scene=''>
-	~~Authors: Liu, W., Mao, Z.W.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DJV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DJV FirstGlance]. <br>
-	~~Description:~~ NMR solution structure of the 2:1 complex of a platinum(II) compound bound to Myc1234 G-quadruplex reveals the mechanism of conformational switch and dynamic binding of G-quadruplex	+	</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=7djv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7djv OCA], [https://pdbe.org/7djv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7djv RCSB], [https://www.ebi.ac.uk/pdbsum/7djv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7djv ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Mao~~, Z.W]]	+	__TOC__
-	[[Category: Liu, W]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Liu W]]
		+	[[Category: Mao ZW]]

OCA at 11:35, 29 December 2021

2021-12-29T11:35:05Z

←Older revision		Revision as of 11:35, 29 December 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Liu, W., Mao, Z.W.		Authors: Liu, W., Mao, Z.W.

OCA at 13:49, 22 December 2021

2021-12-22T13:49:03Z

←Older revision		Revision as of 13:49, 22 December 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7djv is ON HOLD ~~until Paper Publication~~	+	The entry 7djv is ON HOLD

	Authors: Liu, W., Mao, Z.W.		Authors: Liu, W., Mao, Z.W.

OCA at 13:21, 2 June 2021

2021-06-02T13:21:14Z

←Older revision		Revision as of 13:21, 2 June 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Liu, W., Mao, Z.W.		Authors: Liu, W., Mao, Z.W.

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

2020-12-02T05:42:03Z

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

←Older revision

Revision as of 05:42, 2 December 2020

OCA: New page: '''Unreleased structure''' The entry 7djv is ON HOLD Authors: Liu, W., Mao, Z.W. Description: NMR solution structure of the 2:1 complex of a platinum(II) compound bound to Myc1234 G-qu...

2020-12-02T05:42:02Z

New page: '''Unreleased structure''' The entry 7djv is ON HOLD Authors: Liu, W., Mao, Z.W. Description: NMR solution structure of the 2:1 complex of a platinum(II) compound bound to Myc1234 G-qu...

New page

'''Unreleased structure'''

The entry 7djv is ON HOLD

Authors: Liu, W., Mao, Z.W.

Description: NMR solution structure of the 2:1 complex of a platinum(II) compound bound to Myc1234 G-quadruplex reveals the mechanism of conformational switch and dynamic binding of G-quadruplex
[[Category: Unreleased Structures]]
[[Category: Mao, Z.W]]
[[Category: Liu, W]]