5ykn - Revision history

OCA at 08:32, 22 November 2023

2023-11-22T08:32:27Z

←Older revision		Revision as of 08:32, 22 November 2023
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	==crystal structure of Arabidopsis thaliana JMJ14 catalytic domain==		==crystal structure of Arabidopsis thaliana JMJ14 catalytic domain==
-	<StructureSection load='5ykn' size='340' side='right' caption='[[5ykn]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5ykn' size='340' side='right'caption='[[5ykn]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ykn]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Arath Arath~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YKN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YKN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ykn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YKN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=NI:NICKEL+(II)+ION'>NI</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='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~JMJ14, JMJ4, PKDM7B, At4g20400, F9F13.50 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=3702 ARATH])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5ykn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ykn OCA], [~~http~~://pdbe.org/5ykn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ykn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ykn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ykn ProSAT]</span></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=5ykn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ykn OCA], [https://pdbe.org/5ykn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ykn RCSB], [https://www.ebi.ac.uk/pdbsum/5ykn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ykn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/JMJ14_ARATH JMJ14_ARATH]] Transcriptional repressor (PubMed:25578968). Histone demethylase that demethylates 'Lys-4' (H3K4me) of histone H3 with a higher activity for H3K4me3 and H3K4me2 than H3K4me1. No activity on H3K9me3/2, H3K36me3/2 and H3K27me3/2. Represses FT and TSF expression to inhibit the floral transition. Binds around the transcription start site of the FT locus. Involved in the DRM2-mediated maintenance of DNA methylation, but not required for the de novo DNA methylation. Required for demethylating histone H3K4me3 at the target of RNA silencing. Together with NAC051/NAC052 and NAC050, regulates gene expression and flowering time, probably by the promotion of RNA-mediated gene silencing (PubMed:25578968).<ref>PMID:19946624</ref> <ref>PMID:20177424</ref> <ref>PMID:20202164</ref> <ref>PMID:20478993</ref> <ref>PMID:21052090</ref> <ref>PMID:25578968</ref> <ref>PMID:26617990</ref>	+	[https://www.uniprot.org/uniprot/JMJ14_ARATH JMJ14_ARATH] Transcriptional repressor (PubMed:25578968). Histone demethylase that demethylates 'Lys-4' (H3K4me) of histone H3 with a higher activity for H3K4me3 and H3K4me2 than H3K4me1. No activity on H3K9me3/2, H3K36me3/2 and H3K27me3/2. Represses FT and TSF expression to inhibit the floral transition. Binds around the transcription start site of the FT locus. Involved in the DRM2-mediated maintenance of DNA methylation, but not required for the de novo DNA methylation. Required for demethylating histone H3K4me3 at the target of RNA silencing. Together with NAC051/NAC052 and NAC050, regulates gene expression and flowering time, probably by the promotion of RNA-mediated gene silencing (PubMed:25578968).<ref>PMID:19946624</ref> <ref>PMID:20177424</ref> <ref>PMID:20202164</ref> <ref>PMID:20478993</ref> <ref>PMID:21052090</ref> <ref>PMID:25578968</ref> <ref>PMID:26617990</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 5ykn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ykn" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Jumonji domain-containing protein 3D structures\|Jumonji domain-containing protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arath~~]]	+	[[Category: Arabidopsis thaliana]]
-	[[Category: ~~Du, J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Yang, Z~~]]	+	[[Category: Du J]]
-	[[Category: ~~C5hc2 zinc finger]]~~	+	[[Category: Yang Z]]
-	~~[[Category: Gene regulation]]~~	+
-	~~[[Category: H3k4me3 demethylase]]~~	+
-	~~[[Category: Jmj14]]~~	+
-	~~[[Category: Jumonji domain~~]]	+

OCA at 07:13, 28 February 2018

2018-02-28T07:13:23Z

←Older revision		Revision as of 07:13, 28 February 2018
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	<StructureSection load='5ykn' size='340' side='right' caption='[[5ykn]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5ykn' size='340' side='right' caption='[[5ykn]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ykn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YKN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YKN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ykn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YKN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YKN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">JMJ14, JMJ4, PKDM7B, At4g20400, F9F13.50 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=5ykn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ykn OCA], [http://pdbe.org/5ykn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ykn RCSB], [http://www.ebi.ac.uk/pdbsum/5ykn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ykn 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=5ykn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ykn OCA], [http://pdbe.org/5ykn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ykn RCSB], [http://www.ebi.ac.uk/pdbsum/5ykn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ykn ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arath]]
	[[Category: Du, J]]		[[Category: Du, J]]
	[[Category: Yang, Z]]		[[Category: Yang, Z]]

OCA at 08:32, 27 December 2017

2017-12-27T08:32:03Z

←Older revision		Revision as of 08:32, 27 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ykn is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==crystal structure of Arabidopsis thaliana JMJ14 catalytic domain==
		+	<StructureSection load='5ykn' size='340' side='right' caption='[[5ykn]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ykn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YKN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YKN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5ykn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ykn OCA], [http://pdbe.org/5ykn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ykn RCSB], [http://www.ebi.ac.uk/pdbsum/5ykn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ykn ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/JMJ14_ARATH JMJ14_ARATH]] Transcriptional repressor (PubMed:25578968). Histone demethylase that demethylates 'Lys-4' (H3K4me) of histone H3 with a higher activity for H3K4me3 and H3K4me2 than H3K4me1. No activity on H3K9me3/2, H3K36me3/2 and H3K27me3/2. Represses FT and TSF expression to inhibit the floral transition. Binds around the transcription start site of the FT locus. Involved in the DRM2-mediated maintenance of DNA methylation, but not required for the de novo DNA methylation. Required for demethylating histone H3K4me3 at the target of RNA silencing. Together with NAC051/NAC052 and NAC050, regulates gene expression and flowering time, probably by the promotion of RNA-mediated gene silencing (PubMed:25578968).<ref>PMID:19946624</ref> <ref>PMID:20177424</ref> <ref>PMID:20202164</ref> <ref>PMID:20478993</ref> <ref>PMID:21052090</ref> <ref>PMID:25578968</ref> <ref>PMID:26617990</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In chromatin, histone methylation affects the epigenetic regulation of multiple processes in animals and plants and is modulated by the activities of histone methyltransferases and histone demethylases. The jumonji domain-containing histone demethylases have diverse functions and can be classified into several subfamilies. In humans, the jumonji domain-containing Lysine (K)-Specific Demethylase 5/Jumonji and ARID Domain Protein (KDM5/JARID) subfamily demethylases are specific for histone 3 lysine 4 trimethylation (H3K4me3) and are important drug targets for cancer treatment. In Arabidopsis thaliana, the KDM5/JARID subfamily H3K4me3 demethylase JUMONJI 14 (JMJ14) plays important roles in flowering, gene silencing, and DNA methylation. Here, we report the crystal structures of the JMJ14 catalytic domain in both substrate-free and bound forms. The structures reveal that the jumonji and C5HC2 domains contribute to the specific recognition of the H3R2 and H3Q5 to facilitate H3K4me3 substrate specificity. The critical acidic residues are conserved in plants and animals with the corresponding mutations impairing the enzyme activity of both JMJ14 and human KDM5B, indicating a common substrate recognition mechanism for KDM5 subfamily demethylases shared by plants and animals and further informing efforts to design targeted inhibitors of human KDM5.

-	~~Authors~~:	+	Structure of the Arabidopsis JMJ14-H3K4me3 Complex Provides Insight into the Substrate Specificity of KDM5 Subfamily Histone Demethylases.,Yang Z, Qiu Q, Chen W, Jia B, Chen X, Hu H, He K, Deng X, Li S, Tao WA, Cao X, Du J Plant Cell. 2017 Dec 12. pii: tpc.17.00666. doi: 10.1105/tpc.17.00666. PMID:29233856<ref>PMID:29233856</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5ykn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Du, J]]
		+	[[Category: Yang, Z]]
		+	[[Category: C5hc2 zinc finger]]
		+	[[Category: Gene regulation]]
		+	[[Category: H3k4me3 demethylase]]
		+	[[Category: Jmj14]]
		+	[[Category: Jumonji domain]]

OCA at 04:43, 1 November 2017

2017-11-01T04:43:35Z

←Older revision		Revision as of 04:43, 1 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2017-10-25T05:38:31Z

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

←Older revision

Revision as of 05:38, 25 October 2017

OCA: New page: '''Unreleased structure''' The entry 5ykn is ON HOLD Authors: Description: Category: Unreleased Structures

2017-10-25T05:38:30Z

New page: '''Unreleased structure''' The entry 5ykn is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5ykn is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]