4uc4 - Revision history

OCA at 07:27, 27 September 2023

OCA — Wed, 27 Sep 2023 07:27:33 GMT

←Older revision		Revision as of 07:27, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4uc4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UC4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UC4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4uc4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UC4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UC4 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=4uc4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uc4 OCA], [https://pdbe.org/4uc4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uc4 RCSB], [https://www.ebi.ac.uk/pdbsum/4uc4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uc4 ProSAT]</span></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]] 2.5612Å</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=4uc4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uc4 OCA], [https://pdbe.org/4uc4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uc4 RCSB], [https://www.ebi.ac.uk/pdbsum/4uc4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uc4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 08:14, 22 March 2023

OCA — Wed, 22 Mar 2023 08:14:40 GMT

←Older revision		Revision as of 08:14, 22 March 2023
Line 3:		Line 3:
	<StructureSection load='4uc4' size='340' side='right'caption='[[4uc4]], [[Resolution\|resolution]] 2.56Å' scene=''>		<StructureSection load='4uc4' size='340' side='right'caption='[[4uc4]], [[Resolution\|resolution]] 2.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4uc4]] is a 2 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=4UC4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4UC4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4uc4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UC4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UC4 FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KDM4B, JHDM3B, JMJD2B, KIAA0876 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	</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=4uc4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uc4 OCA], [https://pdbe.org/4uc4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uc4 RCSB], [https://www.ebi.ac.uk/pdbsum/4uc4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uc4 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=4uc4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uc4 OCA], [~~http~~://pdbe.org/4uc4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4uc4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4uc4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4uc4 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/KDM4B_HUMAN KDM4B_HUMAN]] Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Only able to demethylate trimethylated H3 'Lys-9', with a weaker activity than KDM4A, KDM4C and KDM4D. Demethylation of Lys residue generates formaldehyde and succinate.<ref>PMID:16603238</ref>	+	[https://www.uniprot.org/uniprot/KDM4B_HUMAN KDM4B_HUMAN] Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Only able to demethylate trimethylated H3 'Lys-9', with a weaker activity than KDM4A, KDM4C and KDM4D. Demethylation of Lys residue generates formaldehyde and succinate.<ref>PMID:16603238</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Denu~~, J M~~]]	+	[[Category: Denu JM]]
-	[[Category: Phillips~~, G N~~]]	+	[[Category: Phillips Jr GN]]
-	[[Category: Su, Z]]	+	[[Category: Su Z]]
-	[[Category: Wang, F]]	+	[[Category: Wang F]]
-	~~[[Category: Chromatin]]~~	+
-	~~[[Category: Replication]]~~	+
-	~~[[Category: Tudor~~]]	+

OCA at 10:24, 25 December 2019

OCA — Wed, 25 Dec 2019 10:24:40 GMT

←Older revision		Revision as of 10:24, 25 December 2019
Line 1:		Line 1:

	==Crystal structure of hybrid tudor domain of human lysine demethylase KDM4B==		==Crystal structure of hybrid tudor domain of human lysine demethylase KDM4B==
-	<StructureSection load='4uc4' size='340' side='right' caption='[[4uc4]], [[Resolution\|resolution]] 2.56Å' scene=''>	+	<StructureSection load='4uc4' size='340' side='right'caption='[[4uc4]], [[Resolution\|resolution]] 2.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4uc4]] is a 2 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=4UC4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UC4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4uc4]] is a 2 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=4UC4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UC4 FirstGlance]. <br>
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4uc4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4uc4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Jumonji domain-containing protein 3D structures\|Jumonji domain-containing protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Denu, J M]]		[[Category: Denu, J M]]
	[[Category: Phillips, G N]]		[[Category: Phillips, G N]]

OCA at 02:59, 16 November 2017

OCA — Thu, 16 Nov 2017 02:59:34 GMT

←Older revision		Revision as of 02:59, 16 November 2017
Line 3:		Line 3:
	<StructureSection load='4uc4' size='340' side='right' caption='[[4uc4]], [[Resolution\|resolution]] 2.56Å' scene=''>		<StructureSection load='4uc4' size='340' side='right' caption='[[4uc4]], [[Resolution\|resolution]] 2.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4uc4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UC4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UC4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4uc4]] is a 2 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=4UC4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UC4 FirstGlance]. <br>
-	</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=4uc4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uc4 OCA], [http://pdbe.org/4uc4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4uc4 RCSB], [http://www.ebi.ac.uk/pdbsum/4uc4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4uc4 ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KDM4B, JHDM3B, JMJD2B, KIAA0876 ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4uc4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uc4 OCA], [http://pdbe.org/4uc4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4uc4 RCSB], [http://www.ebi.ac.uk/pdbsum/4uc4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4uc4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4uc4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4uc4" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Jumonji domain-containing protein\|Jumonji domain-containing protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Denu, J M]]		[[Category: Denu, J M]]
	[[Category: Phillips, G N]]		[[Category: Phillips, G N]]

OCA at 04:17, 4 August 2017

OCA — Fri, 04 Aug 2017 04:17:18 GMT

←Older revision		Revision as of 04:17, 4 August 2017
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4uc4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UC4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UC4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4uc4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UC4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UC4 FirstGlance]. <br>
-	</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=4uc4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uc4 OCA], [http://pdbe.org/4uc4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4uc4 RCSB], [http://www.ebi.ac.uk/pdbsum/4uc4 PDBsum]</span></td></tr>	+	</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=4uc4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uc4 OCA], [http://pdbe.org/4uc4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4uc4 RCSB], [http://www.ebi.ac.uk/pdbsum/4uc4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4uc4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/KDM4B_HUMAN KDM4B_HUMAN]] Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Only able to demethylate trimethylated H3 'Lys-9', with a weaker activity than KDM4A, KDM4C and KDM4D. Demethylation of Lys residue generates formaldehyde and succinate.<ref>PMID:16603238</ref>		[[http://www.uniprot.org/uniprot/KDM4B_HUMAN KDM4B_HUMAN]] Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Only able to demethylate trimethylated H3 'Lys-9', with a weaker activity than KDM4A, KDM4C and KDM4D. Demethylation of Lys residue generates formaldehyde and succinate.<ref>PMID:16603238</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The KDM4 histone demethylases are conserved epigenetic regulators linked to development, spermatogenesis and tumorigenesis. However, how the KDM4 family targets specific chromatin regions is largely unknown. Here, an extensive histone peptide microarray analysis uncovers trimethyl-lysine histone-binding preferences among the closely related KDM4 double tudor domains (DTDs). KDM4A/B DTDs bind strongly to H3K23me3, a poorly understood histone modification recently shown to be enriched in meiotic chromatin of ciliates and nematodes. The 2.28 A co-crystal structure of KDM4A-DTD in complex with H3K23me3 peptide reveals key intermolecular interactions for H3K23me3 recognition. Furthermore, analysis of the 2.56 A KDM4B-DTD crystal structure pinpoints the underlying residues required for exclusive H3K23me3 specificity, an interaction supported by in vivo co-localization of KDM4B and H3K23me3 at heterochromatin in mammalian meiotic and newly postmeiotic spermatocytes. In vitro demethylation assays suggest H3K23me3 binding by KDM4B stimulates H3K36 demethylation. Together, these results provide a possible mechanism whereby H3K23me3-binding by KDM4B directs localized H3K36 demethylation during meiosis and spermatogenesis.
		+
		+	Reader domain specificity and lysine demethylase-4 family function.,Su Z, Wang F, Lee JH, Stephens KE, Papazyan R, Voronina E, Krautkramer KA, Raman A, Thorpe JJ, Boersma MD, Kuznetsov VI, Miller MD, Taverna SD, Phillips GN Jr, Denu JM Nat Commun. 2016 Nov 14;7:13387. doi: 10.1038/ncomms13387. PMID:27841353<ref>PMID:27841353</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4uc4" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 03:42, 11 May 2016

OCA — Wed, 11 May 2016 03:42:58 GMT

←Older revision		Revision as of 03:42, 11 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 4uc4 is ~~ON HOLD~~ ~~until Mar 10 2017~~	+	==Crystal structure of hybrid tudor domain of human lysine demethylase KDM4B==
		+	<StructureSection load='4uc4' size='340' side='right' caption='[[4uc4]], [[Resolution\|resolution]] 2.56Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4uc4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UC4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UC4 FirstGlance]. <br>
		+	</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=4uc4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uc4 OCA], [http://pdbe.org/4uc4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4uc4 RCSB], [http://www.ebi.ac.uk/pdbsum/4uc4 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KDM4B_HUMAN KDM4B_HUMAN]] Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Only able to demethylate trimethylated H3 'Lys-9', with a weaker activity than KDM4A, KDM4C and KDM4D. Demethylation of Lys residue generates formaldehyde and succinate.<ref>PMID:16603238</ref>

-	~~Authors: Wang, F., Su, Z., Denu, J.M., Phillips Jr., G.N.~~	+	==See Also==
-		+	*[[Jumonji domain-containing protein\|Jumonji domain-containing protein]]
-	~~Description: Crystal structure of hybrid tudor~~ domain ~~of human lysine demethylase KDM4B~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
-	[[Category: G.N]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Denu, J M]]
		+	[[Category: Phillips, G N]]
	[[Category: Su, Z]]		[[Category: Su, Z]]
-	[[Category: Denu, J.M]]
	[[Category: Wang, F]]		[[Category: Wang, F]]
-	[[Category: ~~Phillips Jr~~]]	+	[[Category: Chromatin]]
		+	[[Category: Replication]]
		+	[[Category: Tudor]]

OCA at 20:33, 9 March 2016

OCA — Wed, 09 Mar 2016 20:33:20 GMT

←Older revision		Revision as of 20:33, 9 March 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4uc4 is ON HOLD until Mar 03 2017	+	The entry 4uc4 is ON HOLD until Mar 10 2017

	Authors: Wang, F., Su, Z., Denu, J.M., Phillips Jr., G.N.		Authors: Wang, F., Su, Z., Denu, J.M., Phillips Jr., G.N.

OCA at 05:30, 7 January 2016

OCA — Thu, 07 Jan 2016 05:30:01 GMT

←Older revision		Revision as of 05:30, 7 January 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4uc4 is ON HOLD until ~~Jan 01~~ 2017	+	The entry 4uc4 is ON HOLD until Mar 03 2017

	Authors: Wang, F., Su, Z., Denu, J.M., Phillips Jr., G.N.		Authors: Wang, F., Su, Z., Denu, J.M., Phillips Jr., G.N.

OCA at 22:56, 30 November 2015

OCA — Mon, 30 Nov 2015 22:56:00 GMT

←Older revision		Revision as of 22:56, 30 November 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4uc4 is ON HOLD until ~~Nov~~ 01 ~~2016~~	+	The entry 4uc4 is ON HOLD until Jan 01 2017

	Authors: Wang, F., Su, Z., Denu, J.M., Phillips Jr., G.N.		Authors: Wang, F., Su, Z., Denu, J.M., Phillips Jr., G.N.

OCA at 10:20, 8 July 2015

OCA — Wed, 08 Jul 2015 10:20:30 GMT

←Older revision		Revision as of 10:20, 8 July 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4uc4 is ON HOLD until ~~Paper Publication~~	+	The entry 4uc4 is ON HOLD until Nov 01 2016

	Authors: Wang, F., Su, Z., Denu, J.M., Phillips Jr., G.N.		Authors: Wang, F., Su, Z., Denu, J.M., Phillips Jr., G.N.