5zqf - Revision history

OCA at 09:03, 22 November 2023

OCA — Wed, 22 Nov 2023 09:03:43 GMT

←Older revision		Revision as of 09:03, 22 November 2023
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	==Crystal structure of human topoisomerase II beta in complex with 5-iodouridine-containing-DNA in space group P3221==		==Crystal structure of human topoisomerase II beta in complex with 5-iodouridine-containing-DNA in space group P3221==
-	<StructureSection load='5zqf' size='340' side='right' caption='[[5zqf]], [[Resolution\|resolution]] 3.87Å' scene=''>	+	<StructureSection load='5zqf' size='340' side='right'caption='[[5zqf]], [[Resolution\|resolution]] 3.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zqf]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZQF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zqf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZQF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 3.873Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=IU:5-IODOURIDINE-5-MONOPHOSPHATE'>IU</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IU:5-IODOURIDINE-5-MONOPHOSPHATE'>IU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">TOP2B~~ (~~[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]~~)~~</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=5zqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zqf OCA], [https://pdbe.org/5zqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zqf RCSB], [https://www.ebi.ac.uk/pdbsum/5zqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zqf ProSAT]</span></td></tr>
-	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </span></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5zqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zqf OCA], [~~http~~://pdbe.org/5zqf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zqf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zqf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zqf ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TOP2B_HUMAN TOP2B_HUMAN]] Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks. Indirectly involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene.<ref>PMID:10684600</ref> <ref>PMID:12837248</ref>	+	[https://www.uniprot.org/uniprot/TOP2B_HUMAN TOP2B_HUMAN] Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks. Indirectly involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene.<ref>PMID:10684600</ref> <ref>PMID:12837248</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5zqf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5zqf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Topoisomerase 3D structures\|Topoisomerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Chan, N L~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Chen, S F~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Wang, Y R~~]]	+	[[Category: Chan NL]]
-	[[Category: ~~Cleavage complex~~]]	+	[[Category: Chen SF]]
-	[[Category: ~~Dna-gate]]~~	+	[[Category: Wang YR]]
-	~~[[Category: Isomerase-dna complex]]~~	+
-	~~[[Category: Type ii topoisomerase~~]]	+

OCA at 07:40, 21 February 2019

OCA — Thu, 21 Feb 2019 07:40:35 GMT

←Older revision		Revision as of 07:40, 21 February 2019
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	<StructureSection load='5zqf' size='340' side='right' caption='[[5zqf]], [[Resolution\|resolution]] 3.87Å' scene=''>		<StructureSection load='5zqf' size='340' side='right' caption='[[5zqf]], [[Resolution\|resolution]] 3.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zqf]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZQF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zqf]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZQF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IU:5-IODOURIDINE-5-MONOPHOSPHATE'>IU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IU:5-IODOURIDINE-5-MONOPHOSPHATE'>IU</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TOP2B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5zqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zqf OCA], [http://pdbe.org/5zqf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zqf RCSB], [http://www.ebi.ac.uk/pdbsum/5zqf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zqf ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5zqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zqf OCA], [http://pdbe.org/5zqf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zqf RCSB], [http://www.ebi.ac.uk/pdbsum/5zqf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zqf ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/TOP2B_HUMAN TOP2B_HUMAN]] Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks. Indirectly involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene.<ref>PMID:10684600</ref> <ref>PMID:12837248</ref>		[[http://www.uniprot.org/uniprot/TOP2B_HUMAN TOP2B_HUMAN]] Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks. Indirectly involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene.<ref>PMID:10684600</ref> <ref>PMID:12837248</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Type IIA topoisomerases (Top2s) manipulate the handedness of DNA crossovers by introducing a transient and protein-linked double-strand break in one DNA duplex, termed the DNA-gate, whose opening allows another DNA segment to be transported through to change the DNA topology. Despite the central importance of this gate-opening event to Top2 function, the DNA-gate in all reported structures of Top2-DNA complexes is in the closed state. Here we present the crystal structure of a human Top2 DNA-gate in an open conformation, which not only reveals structural characteristics of its DNA-conducting path, but also uncovers unexpected yet functionally significant conformational changes associated with gate-opening. This structure further implicates Top2's preference for a left-handed DNA braid and allows the construction of a model representing the initial entry of another DNA duplex into the DNA-gate. Steered molecular dynamics calculations suggests the Top2-catalyzed DNA passage may be achieved by a rocker-switch-type movement of the DNA-gate.
		+
		+	Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate.,Chen SF, Huang NL, Lin JH, Wu CC, Wang YR, Yu YJ, Gilson MK, Chan NL Nat Commun. 2018 Aug 6;9(1):3085. doi: 10.1038/s41467-018-05406-y. PMID:30082834<ref>PMID:30082834</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5zqf" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Chan, N L]]		[[Category: Chan, N L]]
	[[Category: Chen, S F]]		[[Category: Chen, S F]]

OCA at 21:44, 9 August 2018

OCA — Thu, 09 Aug 2018 21:44:55 GMT

←Older revision		Revision as of 21:44, 9 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5zqf is ON HOLD until Paper Publication~~	+	==Crystal structure of human topoisomerase II beta in complex with 5-iodouridine-containing-DNA in space group P3221==
-		+	<StructureSection load='5zqf' size='340' side='right' caption='[[5zqf]], [[Resolution\|resolution]] 3.87Å' scene=''>
-	~~Authors: Chen, S.F., Wang, Y.R., Chan, N.L.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5zqf]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZQF FirstGlance]. <br>
-	~~Description:~~ Crystal structure of human topoisomerase II beta in complex with 5-iodouridine-containing-DNA in space group P3221	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IU:5-IODOURIDINE-5-MONOPHOSPHATE'>IU</scene></td></tr>
-	[[Category: Chan, N.L]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </span></td></tr>
-	[[Category: Chen, S.F]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5zqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zqf OCA], [http://pdbe.org/5zqf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zqf RCSB], [http://www.ebi.ac.uk/pdbsum/5zqf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zqf ProSAT]</span></td></tr>
-	[[Category: Wang, Y.R]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TOP2B_HUMAN TOP2B_HUMAN]] Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks. Indirectly involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene.<ref>PMID:10684600</ref> <ref>PMID:12837248</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chan, N L]]
		+	[[Category: Chen, S F]]
		+	[[Category: Wang, Y R]]
		+	[[Category: Cleavage complex]]
		+	[[Category: Dna-gate]]
		+	[[Category: Isomerase-dna complex]]
		+	[[Category: Type ii topoisomerase]]

OCA at 06:33, 2 May 2018

OCA — Wed, 02 May 2018 06:33:17 GMT

←Older revision		Revision as of 06:33, 2 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zqf is ON HOLD	+	The entry 5zqf is ON HOLD until Paper Publication

	Authors: Chen, S.F., Wang, Y.R., Chan, N.L.		Authors: Chen, S.F., Wang, Y.R., Chan, N.L.
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	Description: Crystal structure of human topoisomerase II beta in complex with 5-iodouridine-containing-DNA in space group P3221		Description: Crystal structure of human topoisomerase II beta in complex with 5-iodouridine-containing-DNA in space group P3221
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Wang, Y.R]]
	[[Category: Chan, N.L]]		[[Category: Chan, N.L]]
	[[Category: Chen, S.F]]		[[Category: Chen, S.F]]
		+	[[Category: Wang, Y.R]]

OCA: Protected "5zqf" [edit=sysop:move=sysop]

OCA — Wed, 25 Apr 2018 03:55:05 GMT

Protected "5zqf" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:55, 25 April 2018

OCA: New page: '''Unreleased structure''' The entry 5zqf is ON HOLD Authors: Chen, S.F., Wang, Y.R., Chan, N.L. Description: Crystal structure of human topoisomerase II beta in complex with 5-iodouri...

OCA — Wed, 25 Apr 2018 03:55:04 GMT

New page: '''Unreleased structure''' The entry 5zqf is ON HOLD Authors: Chen, S.F., Wang, Y.R., Chan, N.L. Description: Crystal structure of human topoisomerase II beta in complex with 5-iodouri...

New page

'''Unreleased structure'''

The entry 5zqf is ON HOLD

Authors: Chen, S.F., Wang, Y.R., Chan, N.L.

Description: Crystal structure of human topoisomerase II beta in complex with 5-iodouridine-containing-DNA in space group P3221
[[Category: Unreleased Structures]]
[[Category: Wang, Y.R]]
[[Category: Chan, N.L]]
[[Category: Chen, S.F]]