3kva - Revision history

OCA at 08:24, 6 September 2023

OCA — Wed, 06 Sep 2023 08:24:42 GMT

←Older revision		Revision as of 08:24, 6 September 2023
Line 1:		Line 1:

	==Structure of KIAA1718 Jumonji domain in complex with alpha-ketoglutarate==		==Structure of KIAA1718 Jumonji domain in complex with alpha-ketoglutarate==
-	<StructureSection load='3kva' size='340' side='right' caption='[[3kva]], [[Resolution\|resolution]] 2.79Å' scene=''>	+	<StructureSection load='3kva' size='340' side='right'caption='[[3kva]], [[Resolution\|resolution]] 2.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kva]] is a 1 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=3KVA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3KVA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kva]] is a 1 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=3KVA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KVA FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=AKG:2~~-~~OXOGLUTARIC+ACID'>AKG</scene>~~, ~~<scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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]] 2.79Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[3kv5\|3kv5]], [[3kv4\|3kv4]], [[3kv9\|3kv9]], [[3kvb\|3kvb]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>
-	<~~tr id~~='~~gene~~'><~~td class="sblockLbl"~~><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">JHDM1D, KIAA1718 ([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=3kva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kva OCA], [https://pdbe.org/3kva PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kva RCSB], [https://www.ebi.ac.uk/pdbsum/3kva PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kva 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=3kva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kva OCA], [~~http~~://pdbe.org/3kva PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3kva RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3kva PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3kva ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/KDM7A_HUMAN KDM7A_HUMAN]] Histone demethylase required for brain development. Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2 and H3K27me2, respectively) of histone H3 and monomethylated histone H4 'Lys-20' residue (H4K20Me1), thereby playing a central role in histone code. Specifically binds trimethylated 'Lys-4' of histone H3 (H3K4me3), affecting histone demethylase specificity: in presence of H3K4me3, it has no demethylase activity toward H3K9me2, while it has high activity toward H3K27me2. Demethylates H3K9me2 in absence of H3K4me3. Has activity toward H4K20Me1 only when nucleosome is used as a substrate and when not histone octamer is used as substrate.<ref>PMID:20023638</ref> <ref>PMID:20194436</ref> <ref>PMID:20622853</ref>	+	[https://www.uniprot.org/uniprot/KDM7A_HUMAN KDM7A_HUMAN] Histone demethylase required for brain development. Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2 and H3K27me2, respectively) of histone H3 and monomethylated histone H4 'Lys-20' residue (H4K20Me1), thereby playing a central role in histone code. Specifically binds trimethylated 'Lys-4' of histone H3 (H3K4me3), affecting histone demethylase specificity: in presence of H3K4me3, it has no demethylase activity toward H3K9me2, while it has high activity toward H3K27me2. Demethylates H3K9me2 in absence of H3K4me3. Has activity toward H4K20Me1 only when nucleosome is used as a substrate and when not histone octamer is used as substrate.<ref>PMID:20023638</ref> <ref>PMID:20194436</ref> <ref>PMID:20622853</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: Cheng, X]]	+	[[Category: Large Structures]]
-	[[Category: Horton~~, J R~~]]	+	[[Category: Cheng X]]
-	[[Category: Qi~~, H H~~]]	+	[[Category: Horton JR]]
-	[[Category: Shi, Y]]	+	[[Category: Qi HH]]
-	[[Category: Upadhyay~~, A K~~]]	+	[[Category: Shi Y]]
-	[[Category: Zhang, X]]	+	[[Category: Upadhyay AK]]
-	~~[[Category: H3k4me3 binding protein]]~~	+	[[Category: Zhang X]]
-	~~[[Category: Jumonji domain lysine demethylase]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Zinc-finger~~]]	+

OCA at 06:42, 2 January 2019

OCA — Wed, 02 Jan 2019 06:42:58 GMT

←Older revision		Revision as of 06:42, 2 January 2019
Line 1:		Line 1:
		+
	==Structure of KIAA1718 Jumonji domain in complex with alpha-ketoglutarate==		==Structure of KIAA1718 Jumonji domain in complex with alpha-ketoglutarate==
	<StructureSection load='3kva' size='340' side='right' caption='[[3kva]], [[Resolution\|resolution]] 2.79Å' scene=''>		<StructureSection load='3kva' size='340' side='right' caption='[[3kva]], [[Resolution\|resolution]] 2.79Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kv5\|3kv5]], [[3kv4\|3kv4]], [[3kv9\|3kv9]], [[3kvb\|3kvb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kv5\|3kv5]], [[3kv4\|3kv4]], [[3kv9\|3kv9]], [[3kvb\|3kvb]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">JHDM1D, KIAA1718 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">JHDM1D, KIAA1718 ([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=3kva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kva OCA], [http://pdbe.org/3kva PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kva RCSB], [http://www.ebi.ac.uk/pdbsum/3kva PDBsum]</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=3kva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kva OCA], [http://pdbe.org/3kva PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kva RCSB], [http://www.ebi.ac.uk/pdbsum/3kva PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kva ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kv/3kva_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kv/3kva_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 09:15, 9 February 2016

OCA — Tue, 09 Feb 2016 09:15:23 GMT

←Older revision		Revision as of 09:15, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3kva' size='340' side='right' caption='[[3kva]], [[Resolution\|resolution]] 2.79Å' scene=''>		<StructureSection load='3kva' size='340' side='right' caption='[[3kva]], [[Resolution\|resolution]] 2.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kva]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KVA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kva]] is a 1 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=3KVA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KVA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kv5\|3kv5]], [[3kv4\|3kv4]], [[3kv9\|3kv9]], [[3kvb\|3kvb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kv5\|3kv5]], [[3kv4\|3kv4]], [[3kv9\|3kv9]], [[3kvb\|3kvb]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">JHDM1D, KIAA1718 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">JHDM1D, KIAA1718 ([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=3kva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kva OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kva RCSB], [http://www.ebi.ac.uk/pdbsum/3kva PDBsum]</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=3kva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kva OCA], [http://pdbe.org/3kva PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kva RCSB], [http://www.ebi.ac.uk/pdbsum/3kva PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~JHD1D_HUMAN JHD1D_HUMAN~~]] Histone demethylase required for brain development. Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2 and H3K27me2, respectively) of histone H3 and monomethylated histone H4 'Lys-20' residue (H4K20Me1), thereby playing a central role in histone code. Specifically binds trimethylated 'Lys-4' of histone H3 (H3K4me3), affecting histone demethylase specificity: in presence of H3K4me3, it has no demethylase activity toward H3K9me2, while it has high activity toward H3K27me2. Demethylates H3K9me2 in absence of H3K4me3. Has activity toward H4K20Me1 only when nucleosome is used as a substrate and when not histone octamer is used as substrate.<ref>PMID:20023638</ref> <ref>PMID:20194436</ref> <ref>PMID:20622853</ref>	+	[[http://www.uniprot.org/uniprot/KDM7A_HUMAN KDM7A_HUMAN]] Histone demethylase required for brain development. Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2 and H3K27me2, respectively) of histone H3 and monomethylated histone H4 'Lys-20' residue (H4K20Me1), thereby playing a central role in histone code. Specifically binds trimethylated 'Lys-4' of histone H3 (H3K4me3), affecting histone demethylase specificity: in presence of H3K4me3, it has no demethylase activity toward H3K9me2, while it has high activity toward H3K27me2. Demethylates H3K9me2 in absence of H3K4me3. Has activity toward H4K20Me1 only when nucleosome is used as a substrate and when not histone octamer is used as substrate.<ref>PMID:20023638</ref> <ref>PMID:20194436</ref> <ref>PMID:20622853</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3kva ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3kva" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Cheng, X]]		[[Category: Cheng, X]]
	[[Category: Horton, J R]]		[[Category: Horton, J R]]

OCA at 05:57, 25 December 2014

OCA — Thu, 25 Dec 2014 05:57:56 GMT

←Older revision		Revision as of 05:57, 25 December 2014
Line 8:		Line 8:
	<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=3kva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kva OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kva RCSB], [http://www.ebi.ac.uk/pdbsum/3kva PDBsum]</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=3kva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kva OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kva RCSB], [http://www.ebi.ac.uk/pdbsum/3kva PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/JHD1D_HUMAN JHD1D_HUMAN]] Histone demethylase required for brain development. Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2 and H3K27me2, respectively) of histone H3 and monomethylated histone H4 'Lys-20' residue (H4K20Me1), thereby playing a central role in histone code. Specifically binds trimethylated 'Lys-4' of histone H3 (H3K4me3), affecting histone demethylase specificity: in presence of H3K4me3, it has no demethylase activity toward H3K9me2, while it has high activity toward H3K27me2. Demethylates H3K9me2 in absence of H3K4me3. Has activity toward H4K20Me1 only when nucleosome is used as a substrate and when not histone octamer is used as substrate.<ref>PMID:20023638</ref> <ref>PMID:20194436</ref> <ref>PMID:20622853</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 16:45, 18 December 2014

OCA — Thu, 18 Dec 2014 16:45:19 GMT

←Older revision		Revision as of 16:45, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3kva\| PDB=3kva \| SCENE= }}~~	+	==Structure of KIAA1718 Jumonji domain in complex with alpha-ketoglutarate==
-	===Structure of KIAA1718 Jumonji domain in complex with alpha-ketoglutarate===	+	<StructureSection load='3kva' size='340' side='right' caption='[[3kva]], [[Resolution\|resolution]] 2.79Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20023638}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3kva]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KVA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kv5\|3kv5]], [[3kv4\|3kv4]], [[3kv9\|3kv9]], [[3kvb\|3kvb]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">JHDM1D, KIAA1718 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3kva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kva OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kva RCSB], [http://www.ebi.ac.uk/pdbsum/3kva PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kv/3kva_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Combinatorial readout of multiple covalent histone modifications is poorly understood. We provide insights into how an activating histone mark, in combination with linked repressive marks, is differentially 'read' by two related human demethylases, PHF8 and KIAA1718 (also known as JHDM1D). Both enzymes harbor a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2. The presence of H3K4me3 on the same peptide as H3K9me2 makes the doubly methylated peptide a markedly better substrate of PHF8, whereas the presence of H3K4me3 has the opposite effect, diminishing the H3K9me2 demethylase activity of KIAA1718 without adversely affecting its H3K27me2 activity. The difference in substrate specificity between the two is explained by PHF8 adopting a bent conformation, allowing each of its domains to engage its respective target, whereas KIAA1718 adopts an extended conformation, which prevents its access to H3K9me2 by its jumonji domain when its PHD engages H3K4me3.

-	~~==About this Structure==~~	+	Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases.,Horton JR, Upadhyay AK, Qi HH, Zhang X, Shi Y, Cheng X Nat Struct Mol Biol. 2010 Jan;17(1):38-43. Epub 2009 Dec 20. PMID:20023638<ref>PMID:20023638</ref>
-	~~[[3kva]] is~~ a 1 ~~chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3KVA OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:020023638</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Cheng, X.]]	+	[[Category: Cheng, X]]
-	[[Category: Horton, J R.]]	+	[[Category: Horton, J R]]
-	[[Category: Qi, H H.]]	+	[[Category: Qi, H H]]
-	[[Category: Shi, Y.]]	+	[[Category: Shi, Y]]
-	[[Category: Upadhyay, A K.]]	+	[[Category: Upadhyay, A K]]
-	[[Category: Zhang, X.]]	+	[[Category: Zhang, X]]
	[[Category: H3k4me3 binding protein]]		[[Category: H3k4me3 binding protein]]
	[[Category: Jumonji domain lysine demethylase]]		[[Category: Jumonji domain lysine demethylase]]

OCA: Protected "3kva" [edit=sysop:move=sysop]

OCA — Thu, 04 Apr 2013 20:19:50 GMT

Protected "3kva" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:19, 4 April 2013

OCA at 20:19, 4 April 2013

OCA — Thu, 04 Apr 2013 20:19:49 GMT

←Older revision		Revision as of 20:19, 4 April 2013
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-	{{Seed}}
-	[[Image:3kva.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3kva", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3kva\| PDB=3kva \| SCENE= }}		{{STRUCTURE_3kva\| PDB=3kva \| SCENE= }}
-
	===Structure of KIAA1718 Jumonji domain in complex with alpha-ketoglutarate===		===Structure of KIAA1718 Jumonji domain in complex with alpha-ketoglutarate===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20023638}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20023638 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20023638}}		{{ABSTRACT_PUBMED_20023638}}

	==About this Structure==		==About this Structure==
-	~~3KVA~~ is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVA OCA].	+	[[3kva]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVA OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20023638~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020023638</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Cheng, X.]]		[[Category: Cheng, X.]]
Line 31:		Line 15:
	[[Category: Upadhyay, A K.]]		[[Category: Upadhyay, A K.]]
	[[Category: Zhang, X.]]		[[Category: Zhang, X.]]
		+	[[Category: H3k4me3 binding protein]]
	[[Category: Jumonji domain lysine demethylase]]		[[Category: Jumonji domain lysine demethylase]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
-	[[Category: ~~Zinc~~]]	+	[[Category: Transferase]]
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 10 17:45:06 2010''

OCA at 15:45, 10 February 2010

OCA — Wed, 10 Feb 2010 15:45:06 GMT

←Older revision		Revision as of 15:45, 10 February 2010
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	{{Seed}}		{{Seed}}
-	[[Image:3kva.~~jpg~~\|left\|200px]]	+	[[Image:3kva.png\|left\|200px]]

	<!--		<!--
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	===Structure of KIAA1718 Jumonji domain in complex with alpha-ketoglutarate===		===Structure of KIAA1718 Jumonji domain in complex with alpha-ketoglutarate===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20023638}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20023638 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20023638}}

	==About this Structure==		==About this Structure==
-	3KVA is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVA OCA].	+	3KVA is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVA OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20023638</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Cheng, X.]]		[[Category: Cheng, X.]]
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	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Dec 23~~ 10:25:~~10 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 10 17:45:06 2010''

OCA at 08:25, 23 December 2009

OCA — Wed, 23 Dec 2009 08:25:11 GMT

←Older revision		Revision as of 08:25, 23 December 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3kva.jpg\|left\|200px]]

-	The ~~entry 3kva~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3kva", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3kva\| PDB=3kva \| SCENE= }}

-	~~Authors: Horton, J.R., Upadhyay, A.K., Qi, H.H., Zhang, X., Shi, Y., Cheng, X.~~	+	===Structure of KIAA1718 Jumonji domain in complex with alpha-ketoglutarate===

-	Description: Structure of KIAA1718 Jumonji domain in complex with alpha-ketoglutarate

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec ~~9 14~~:45:02 2009''	+	==About this Structure==
		+	3KVA is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVA OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Cheng, X.]]
		+	[[Category: Horton, J R.]]
		+	[[Category: Qi, H H.]]
		+	[[Category: Shi, Y.]]
		+	[[Category: Upadhyay, A K.]]
		+	[[Category: Zhang, X.]]
		+	[[Category: Jumonji domain lysine demethylase]]
		+	[[Category: Metal-binding]]
		+	[[Category: Zinc]]
		+	[[Category: Zinc-finger]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 23 10:25:10 2009''

OCA: New page: '''Unreleased structure''' The entry 3kva is ON HOLD Authors: Horton, J.R., Upadhyay, A.K., Qi, H.H., Zhang, X., Shi, Y., Cheng, X. Description: Structure of KIAA1718 Jumonji domain in...

OCA — Wed, 09 Dec 2009 12:45:02 GMT

New page: '''Unreleased structure''' The entry 3kva is ON HOLD Authors: Horton, J.R., Upadhyay, A.K., Qi, H.H., Zhang, X., Shi, Y., Cheng, X. Description: Structure of KIAA1718 Jumonji domain in...

New page

'''Unreleased structure'''

The entry 3kva is ON HOLD

Authors: Horton, J.R., Upadhyay, A.K., Qi, H.H., Zhang, X., Shi, Y., Cheng, X.

Description: Structure of KIAA1718 Jumonji domain in complex with alpha-ketoglutarate

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 9 14:45:02 2009''