3n9q - Revision history

OCA at 16:44, 1 November 2023

OCA — Wed, 01 Nov 2023 16:44:40 GMT

←Older revision		Revision as of 16:44, 1 November 2023
Line 1:		Line 1:

	==ceKDM7A from C.elegans, complex with H3K4me3 peptide, H3K27me2 peptide and NOG==		==ceKDM7A from C.elegans, complex with H3K4me3 peptide, H3K27me2 peptide and NOG==
-	<StructureSection load='3n9q' size='340' side='right' caption='[[3n9q]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='3n9q' size='340' side='right'caption='[[3n9q]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3n9q]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Caeel Caeel~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N9Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3N9Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3n9q]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N9Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N9Q FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=FE2:FE+(II)+ION'~~>~~FE2</scene>, <scene name='pdbligand=OGA:N~~-~~OXALYLGLYCINE'>OGA</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.3Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[3n9l\|3n9l]]~~, ~~[[3n9m\|3n9m]], [[3n9n\|3n9n]], [[3n9o\|3n9o]], [[3n9p\|3n9p]]~~<~~/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=3n9q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n9q OCA], [https://pdbe.org/3n9q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n9q RCSB], [https://www.ebi.ac.uk/pdbsum/3n9q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n9q ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">F29B9.2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 CAEEL])</td></tr>~~	+
-	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Histone_H3]-lysine-36_demethylase [Histone H3]-lysine-36 demethylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.27 1.14.11.27] </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=3n9q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n9q OCA], [~~http~~://pdbe.org/3n9q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3n9q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3n9q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3n9q ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/KDM7_CAEEL KDM7_CAEEL]] Histone demethylase required for nervous system development. Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2 and H3K27me2, respectively) of histone H3, thereby playing a central role in histone code.<ref>PMID:20567262</ref> <ref>PMID:20346720</ref> <ref>PMID:20567261</ref>	+	[https://www.uniprot.org/uniprot/KDM7_CAEEL KDM7_CAEEL] Histone demethylase required for nervous system development. Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2 and H3K27me2, respectively) of histone H3, thereby playing a central role in histone code.<ref>PMID:20567262</ref> <ref>PMID:20346720</ref> <ref>PMID:20567261</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Caeel~~]]	+	[[Category: Caenorhabditis elegans]]
-	[[Category: Chen~~, C D~~]]	+	[[Category: Large Structures]]
-	[[Category: Hou, H]]	+	[[Category: Chen CD]]
-	[[Category: Hu, L]]	+	[[Category: Hou H]]
-	[[Category: Wang, P]]	+	[[Category: Hu L]]
-	[[Category: Xu, Y]]	+	[[Category: Wang P]]
-	[[Category: Yang, Y]]	+	[[Category: Xu Y]]
-	~~[[Category: Demethylase]]~~	+	[[Category: Yang Y]]
-	~~[[Category: Histone]]~~	+
-	~~[[Category: Jmjc]]~~	+
-	~~[[Category: Methylation]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Phd~~]]	+

OCA at 13:03, 16 January 2019

OCA — Wed, 16 Jan 2019 13:03:36 GMT

←Older revision		Revision as of 13:03, 16 January 2019
Line 17:		Line 17:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n9/3n9q_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n9/3n9q_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 21:24, 4 August 2016

OCA — Thu, 04 Aug 2016 21:24:10 GMT

←Older revision		Revision as of 21:24, 4 August 2016
Line 1:		Line 1:
		+
	==ceKDM7A from C.elegans, complex with H3K4me3 peptide, H3K27me2 peptide and NOG==		==ceKDM7A from C.elegans, complex with H3K4me3 peptide, H3K27me2 peptide and NOG==
	<StructureSection load='3n9q' size='340' side='right' caption='[[3n9q]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3n9q' size='340' side='right' caption='[[3n9q]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3n9q]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Caenorhabditis_elegans Caenorhabditis elegans~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N9Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3N9Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3n9q]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Caeel Caeel]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N9Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3N9Q FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3n9l\|3n9l]], [[3n9m\|3n9m]], [[3n9n\|3n9n]], [[3n9o\|3n9o]], [[3n9p\|3n9p]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3n9l\|3n9l]], [[3n9m\|3n9m]], [[3n9n\|3n9n]], [[3n9o\|3n9o]], [[3n9p\|3n9p]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">F29B9.2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 ~~Caenorhabditis elegans~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">F29B9.2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 CAEEL])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Histone_H3]-lysine-36_demethylase [Histone H3]-lysine-36 demethylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.27 1.14.11.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Histone_H3]-lysine-36_demethylase [Histone H3]-lysine-36 demethylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.27 1.14.11.27] </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=3n9q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n9q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3n9q RCSB], [http://www.ebi.ac.uk/pdbsum/3n9q 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=3n9q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n9q OCA], [http://pdbe.org/3n9q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3n9q RCSB], [http://www.ebi.ac.uk/pdbsum/3n9q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3n9q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~Q9GYI0_CAEEL Q9GYI0_CAEEL~~]] Histone demethylase required for nervous system development. Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2 and H3K27me2, respectively) of histone H3, thereby playing a central role in histone code.<ref>PMID:20567262</ref> <ref>PMID:20346720</ref> <ref>PMID:20567261</ref>	+	[[http://www.uniprot.org/uniprot/KDM7_CAEEL KDM7_CAEEL]] Histone demethylase required for nervous system development. Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2 and H3K27me2, respectively) of histone H3, thereby playing a central role in histone code.<ref>PMID:20567262</ref> <ref>PMID:20346720</ref> <ref>PMID:20567261</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 21:
	<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=3n9q ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 31:
	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 3n9q" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Caenorhabditis elegans~~]]	+	[[Category: Caeel]]
	[[Category: Chen, C D]]		[[Category: Chen, C D]]
	[[Category: Hou, H]]		[[Category: Hou, H]]

OCA at 13:15, 25 December 2014

OCA — Thu, 25 Dec 2014 13:15:54 GMT

←Older revision		Revision as of 13:15, 25 December 2014
Line 10:		Line 10:
	<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=3n9q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n9q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3n9q RCSB], [http://www.ebi.ac.uk/pdbsum/3n9q 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=3n9q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n9q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3n9q RCSB], [http://www.ebi.ac.uk/pdbsum/3n9q PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q9GYI0_CAEEL Q9GYI0_CAEEL]] Histone demethylase required for nervous system development. Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2 and H3K27me2, respectively) of histone H3, thereby playing a central role in histone code.<ref>PMID:20567262</ref> <ref>PMID:20346720</ref> <ref>PMID:20567261</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 14:53, 18 December 2014

OCA — Thu, 18 Dec 2014 14:53:20 GMT

←Older revision		Revision as of 14:53, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3n9q\| PDB=3n9q \| SCENE= }}~~	+	==ceKDM7A from C.elegans, complex with H3K4me3 peptide, H3K27me2 peptide and NOG==
-	===ceKDM7A from C.elegans, complex with H3K4me3 peptide, H3K27me2 peptide and NOG===	+	<StructureSection load='3n9q' size='340' side='right' caption='[[3n9q]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20567261}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3n9q]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N9Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3N9Q FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3n9l\|3n9l]], [[3n9m\|3n9m]], [[3n9n\|3n9n]], [[3n9o\|3n9o]], [[3n9p\|3n9p]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">F29B9.2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 Caenorhabditis elegans])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Histone_H3]-lysine-36_demethylase [Histone H3]-lysine-36 demethylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.27 1.14.11.27] </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=3n9q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n9q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3n9q RCSB], [http://www.ebi.ac.uk/pdbsum/3n9q 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/n9/3n9q_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 ==
		+	Histone lysine methylation can be removed by JmjC domain-containing proteins in a sequence- and methylation-state-specific manner. However, how substrate specificity is determined and how the enzymes are regulated were largely unknown. We recently found that ceKDM7A, a PHD- and JmjC domain-containing protein, is a histone demethylase specific for H3K9me2 and H3K27me2, and the PHD finger binding to H3K4me3 guides the demethylation activity in vivo. To provide structural insight into the molecular mechanisms for the enzymatic activity and the function of the PHD finger, we solved six crystal structures of the enzyme in apo form and in complex with single or two peptides containing various combinations of H3K4me3, H3K9me2, and H3K27me2 modifications. The structures indicate that H3K9me2 and H3K27me2 interact with ceKDM7A in a similar fashion, and that the peptide-binding specificity is determined by a network of specific interactions. The geometrical measurement of the structures also revealed that H3K4me3 associated with the PHD finger and H3K9me2 bound to the JmjC domain are from two separate molecules, suggesting a trans-histone peptide-binding mechanism. Thus, our systemic structural studies reveal not only the substrate recognition by the catalytic domain but also more importantly, the molecular mechanism of dual specificity of ceDKM7A for both H3K9me2 and H3K27me2.

-	~~==Function==~~	+	Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans.,Yang Y, Hu L, Wang P, Hou H, Lin Y, Liu Y, Li Z, Gong R, Feng X, Zhou L, Zhang W, Dong Y, Yang H, Lin H, Wang Y, Chen CD, Xu Y Cell Res. 2010 Aug;20(8):886-98. Epub 2010 Jun 22. PMID:20567261<ref>PMID:20567261</ref>
-	~~[[http://www.uniprot.org/uniprot/Q9GYI0_CAEEL Q9GYI0_CAEEL]] Histone~~ demethylase ~~required for nervous system development~~. ~~Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2 and H3K27me2~~, ~~respectively) of histone H3~~, ~~thereby playing a central role in histone code~~.~~<ref>PMID~~:~~20567262</ref> <ref>~~PMID:~~20346720</ref>~~ <ref>PMID:20567261</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3n9q]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3N9Q OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:020567261</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Caenorhabditis elegans]]		[[Category: Caenorhabditis elegans]]
-	[[Category: Chen, C D.]]	+	[[Category: Chen, C D]]
-	[[Category: Hou, H.]]	+	[[Category: Hou, H]]
-	[[Category: Hu, L.]]	+	[[Category: Hu, L]]
-	[[Category: Wang, P.]]	+	[[Category: Wang, P]]
-	[[Category: Xu, Y.]]	+	[[Category: Xu, Y]]
-	[[Category: Yang, Y.]]	+	[[Category: Yang, Y]]
	[[Category: Demethylase]]		[[Category: Demethylase]]
	[[Category: Histone]]		[[Category: Histone]]

OCA: Protected "3n9q" [edit=sysop:move=sysop]

OCA — Wed, 17 Apr 2013 20:53:52 GMT

Protected "3n9q" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:53, 17 April 2013

OCA at 20:53, 17 April 2013

OCA — Wed, 17 Apr 2013 20:53:50 GMT

←Older revision		Revision as of 20:53, 17 April 2013
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-	{{Seed}}
-	[[Image:3n9q.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3n9q", 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_3n9q\| PDB=3n9q \| SCENE= }}		{{STRUCTURE_3n9q\| PDB=3n9q \| SCENE= }}
-
	===ceKDM7A from C.elegans, complex with H3K4me3 peptide, H3K27me2 peptide and NOG===		===ceKDM7A from C.elegans, complex with H3K4me3 peptide, H3K27me2 peptide and NOG===
		+	{{ABSTRACT_PUBMED_20567261}}

-		+	==Function==
-	~~<!--~~	+	[[http://www.uniprot.org/uniprot/Q9GYI0_CAEEL Q9GYI0_CAEEL]] Histone demethylase required for nervous system development. Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2 and H3K27me2, respectively) of histone H3, thereby playing a central role in histone code.<ref>PMID:20567262</ref> <ref>PMID:20346720</ref> <ref>PMID:20567261</ref>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_20567261}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov), where 20567261 is the PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_20567261}}~~	+

	==About this Structure==		==About this Structure==
-	~~3N9Q~~ is a 3 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N9Q OCA].	+	[[3n9q]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N9Q OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20567261~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020567261</ref><references group="xtra"/><references/>
	[[Category: Caenorhabditis elegans]]		[[Category: Caenorhabditis elegans]]
	[[Category: Chen, C D.]]		[[Category: Chen, C D.]]
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	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Phd]]		[[Category: Phd]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Aug 12 00:13:36 2010''

OCA at 20:06, 11 August 2010

OCA — Wed, 11 Aug 2010 20:06:19 GMT

←Older revision		Revision as of 20:06, 11 August 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3n9q.~~jpg~~\|left\|200px]]	+	[[Image:3n9q.png\|left\|200px]]

	<!--		<!--
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	===ceKDM7A from C.elegans, complex with H3K4me3 peptide, H3K27me2 peptide and NOG===		===ceKDM7A from C.elegans, complex with H3K4me3 peptide, H3K27me2 peptide and NOG===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20567261}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20567261 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20567261}}

	==About this Structure==		==About this Structure==
	3N9Q is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N9Q OCA].		3N9Q is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N9Q OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20567261</ref><references group="xtra"/>
	[[Category: Caenorhabditis elegans]]		[[Category: Caenorhabditis elegans]]
	[[Category: Chen, C D.]]		[[Category: Chen, C D.]]
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	[[Category: Phd]]		[[Category: Phd]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jun 30 13~~:51:14 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Aug 12 00:13:36 2010''

OCA at 09:45, 30 June 2010

OCA — Wed, 30 Jun 2010 09:45:39 GMT

←Older revision		Revision as of 09:45, 30 June 2010
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3n9q.jpg\|left\|200px]]

-	The ~~entry 3n9q~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3n9q", 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_3n9q\| PDB=3n9q \| SCENE= }}

-	~~Authors: Yang, Y~~., Hu, ~~L., Wang, P., Hou, H., Lin, Y., Liu, Y.~~	+	===ceKDM7A from C.elegans, complex with H3K4me3 peptide, H3K27me2 peptide and NOG===

-	Description: Structural insights into a dual specificity histone demethylase ceKDM7A from C.elegans

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun ~~23 08~~:42:30 2010''	+	==About this Structure==
		+	3N9Q is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N9Q OCA].
		+	[[Category: Caenorhabditis elegans]]
		+	[[Category: Chen, C D.]]
		+	[[Category: Hou, H.]]
		+	[[Category: Hu, L.]]
		+	[[Category: Wang, P.]]
		+	[[Category: Xu, Y.]]
		+	[[Category: Yang, Y.]]
		+	[[Category: Demethylase]]
		+	[[Category: Histone]]
		+	[[Category: Jmjc]]
		+	[[Category: Methylation]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Phd]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 30 13:51:14 2010''

OCA at 04:37, 23 June 2010

OCA — Wed, 23 Jun 2010 04:37:11 GMT

←Older revision		Revision as of 04:37, 23 June 2010
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	The entry 3n9q is ON HOLD		The entry 3n9q is ON HOLD

-	Authors: Yang,~~Ying~~, Hu,~~Lulu~~, Wang,~~Ping~~, Hou,~~Haifeng~~, Lin,~~Yan~~, Liu,Yi	+	Authors: Yang, Y., Hu, L., Wang, P., Hou, H., Lin, Y., Liu, Y.

-	Description: Structural insights into a dual specificity histone demethylase ceKDM7A from C. elegans.	+	Description: Structural insights into a dual specificity histone demethylase ceKDM7A from C.elegans

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Jun ~~10 10~~:59:01 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 23 08:42:30 2010''