4igo - Revision history

OCA at 14:15, 8 November 2023

2023-11-08T14:15:46Z

←Older revision		Revision as of 14:15, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4igo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IGO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IGO FirstGlance]. <br>		<table><tr><td colspan='2'>[[4igo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IGO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IGO FirstGlance]. <br>
-	</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=FE:FE+(III)+ION'>FE</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]] 2.4Å</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=FE:FE+(III)+ION'>FE</scene></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=4igo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4igo OCA], [https://pdbe.org/4igo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4igo RCSB], [https://www.ebi.ac.uk/pdbsum/4igo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4igo 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=4igo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4igo OCA], [https://pdbe.org/4igo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4igo RCSB], [https://www.ebi.ac.uk/pdbsum/4igo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4igo ProSAT]</span></td></tr>
	</table>		</table>

OCA at 20:43, 16 November 2022

2022-11-16T20:43:49Z

←Older revision		Revision as of 20:43, 16 November 2022
Line 1:		Line 1:

	==Histone H3 Lysine 4 Demethylating rice Rice JMJ703 in complex with alpha-KG==		==Histone H3 Lysine 4 Demethylating rice Rice JMJ703 in complex with alpha-KG==
-	<StructureSection load='4igo' size='340' side='right' caption='[[4igo]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='4igo' size='340' side='right'caption='[[4igo]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4igo]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Japanese_rice Japanese rice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IGO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4IGO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4igo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IGO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IGO 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=FE:FE+(III)+ION'>FE</scene>~~</td></tr>~~	+	</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=FE:FE+(III)+ION'>FE</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4igp\|4igp]], [[4igq\|4igq]]</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=4igo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4igo OCA], [https://pdbe.org/4igo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4igo RCSB], [https://www.ebi.ac.uk/pdbsum/4igo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4igo ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">P0617H07.8, Os05g0196500 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</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=4igo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4igo OCA], [~~http~~://pdbe.org/4igo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4igo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4igo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4igo ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/JM703_ORYSJ JM703_ORYSJ] Histone demethylase that demethylates 'Lys-4' (H3K4me) of histone H3 with a specific activity for H3K4me3, H3K4me2 and H3K4me1. No activity on H3K9me3/2/1, H3K27me3/2/1 and H3K36me3/2/1. Involved in the control of stem elongation by regulating methylation states of H3K4me3 on cytokinin oxidase (CKX) gene family, which may cause increased expression of CKX genes and reduced cytokinin levels. Prevents ectopic retrotransposition by regulating the levels of H3K4me3 in two non-LTR retrotransposons KARMA and LINE-1 (L1) and reinforcing their repressed states.<ref>PMID:23319643</ref> <ref>PMID:23357881</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Japanese rice~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Chen, Q F~~]]	+	[[Category: Oryza sativa Japonica Group]]
-	[[Category: Chen~~, X S~~]]	+	[[Category: Chen QF]]
-	[[Category: ~~Lou, Z Y~~]]	+	[[Category: Chen XS]]
-	[[Category: ~~Wang, Q~~]]	+	[[Category: Lou ZY]]
-	[[Category: ~~Zhang, F B~~]]	+	[[Category: Wang Q]]
-	[[Category: Zhang~~, Q F~~]]	+	[[Category: Zhang FB]]
-	[[Category: ~~Zhou, D X~~]]	+	[[Category: Zhang QF]]
-	[[Category: ~~Histone demethylase]]~~	+	[[Category: Zhou DX]]
-	~~[[Category: Jumonjic]]~~	+
-	~~[[Category: Structural protein~~]]	+

OCA at 13:40, 5 August 2016

2016-08-05T13:40:58Z

←Older revision		Revision as of 13:40, 5 August 2016
Line 1:		Line 1:
		+
	==Histone H3 Lysine 4 Demethylating rice Rice JMJ703 in complex with alpha-KG==		==Histone H3 Lysine 4 Demethylating rice Rice JMJ703 in complex with alpha-KG==
	<StructureSection load='4igo' size='340' side='right' caption='[[4igo]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4igo' size='340' side='right' caption='[[4igo]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4igo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Oryza_sativa_japonica_group Oryza sativa japonica group~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IGO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IGO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4igo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IGO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IGO 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=FE:FE+(III)+ION'>FE</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=FE:FE+(III)+ION'>FE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4igp\|4igp]], [[4igq\|4igq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4igp\|4igp]], [[4igq\|4igq]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">P0617H07.8, Os05g0196500 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 ~~Oryza sativa Japonica Group~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">P0617H07.8, Os05g0196500 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</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=4igo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4igo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4igo RCSB], [http://www.ebi.ac.uk/pdbsum/4igo 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=4igo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4igo OCA], [http://pdbe.org/4igo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4igo RCSB], [http://www.ebi.ac.uk/pdbsum/4igo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4igo ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4igo" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Oryza sativa japonica group~~]]	+	[[Category: Japanese rice]]
	[[Category: Chen, Q F]]		[[Category: Chen, Q F]]
	[[Category: Chen, X S]]		[[Category: Chen, X S]]

OCA at 12:45, 21 December 2014

2014-12-21T12:45:34Z

←Older revision		Revision as of 12:45, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4igo\| PDB=4igo \| SCENE= }}~~	+	==Histone H3 Lysine 4 Demethylating rice Rice JMJ703 in complex with alpha-KG==
-	===Histone H3 Lysine 4 Demethylating rice Rice JMJ703 in complex with alpha-KG===	+	<StructureSection load='4igo' size='340' side='right' caption='[[4igo]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23357881}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4igo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Oryza_sativa_japonica_group Oryza sativa japonica group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IGO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IGO 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=FE:FE+(III)+ION'>FE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4igp\|4igp]], [[4igq\|4igq]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">P0617H07.8, Os05g0196500 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Oryza sativa Japonica Group])</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=4igo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4igo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4igo RCSB], [http://www.ebi.ac.uk/pdbsum/4igo PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Histone lysine methylation is an important epigenetic modification in regulating chromatin structure and gene expression. Histone H3 lysine 4 methylation (H3K4me), which can be in a mono-, di-, or trimethylated state, has been shown to play an important role in gene expression involved in plant developmental control and stress adaptation. However, the resetting mechanism of this epigenetic modification is not yet fully understood. In this work, we identified a JmjC domain-containing protein, JMJ703, as a histone lysine demethylase that specifically reverses all three forms of H3K4me in rice. Loss-of-function mutation of the gene affected stem elongation and plant growth, which may be related to increased expression of cytokinin oxidase genes in the mutant. Analysis of crystal structure of the catalytic core domain (c-JMJ703) of the protein revealed a general structural similarity with mammalian and yeast JMJD2 proteins that are H3K9 and H3K36 demethylases. However, several specific features were observed in the structure of c-JMJ703. Key residues that interact with cofactors Fe(II) and N-oxalylglycine and the methylated H3K4 substrate peptide were identified and were shown to be essential for the demethylase activity in vivo. Several key residues are specifically conserved in known H3K4 demethylases, suggesting that they may be involved in the specificity for H3K4 demethylation.

-	~~==About this Structure==~~	+	Structural basis of a histone H3 lysine 4 demethylase required for stem elongation in rice.,Chen Q, Chen X, Wang Q, Zhang F, Lou Z, Zhang Q, Zhou DX PLoS Genet. 2013 Jan;9(1):e1003239. doi: 10.1371/journal.pgen.1003239. Epub 2013 , Jan 24. PMID:23357881<ref>PMID:23357881</ref>
-	~~[[4igo]] is~~ a 1 ~~chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org~~/~~wiki/Oryza_sativa_japonica_group Oryza sativa japonica group]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id~~=~~4IGO OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Oryza sativa japonica group]]		[[Category: Oryza sativa japonica group]]
-	[[Category: Chen, Q F.]]	+	[[Category: Chen, Q F]]
-	[[Category: Chen, X S.]]	+	[[Category: Chen, X S]]
-	[[Category: Lou, Z Y.]]	+	[[Category: Lou, Z Y]]
-	[[Category: Wang, Q.]]	+	[[Category: Wang, Q]]
-	[[Category: Zhang, F B.]]	+	[[Category: Zhang, F B]]
-	[[Category: Zhang, Q F.]]	+	[[Category: Zhang, Q F]]
-	[[Category: Zhou, D X.]]	+	[[Category: Zhou, D X]]
	[[Category: Histone demethylase]]		[[Category: Histone demethylase]]
	[[Category: Jumonjic]]		[[Category: Jumonjic]]
	[[Category: Structural protein]]		[[Category: Structural protein]]

OCA at 01:29, 4 April 2013

2013-04-04T01:29:33Z

←Older revision		Revision as of 01:29, 4 April 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4igo\| PDB=4igo \| SCENE= }}
		+	===Histone H3 Lysine 4 Demethylating rice Rice JMJ703 in complex with alpha-KG===
		+	{{ABSTRACT_PUBMED_23357881}}

-	~~The entry~~ 4igo is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4igo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Oryza_sativa_japonica_group Oryza sativa japonica group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IGO OCA].
-	~~Authors~~: Chen, Q.F., Chen, X.S., Wang, Q., Zhang, F.B.~~, Lou, Z.Y.,~~ Zhang, Q.F., Zhou, D.X.	+	[[Category: Oryza sativa japonica group]]
-		+	[[Category: Chen, Q F.]]
-	~~Description~~: Histone ~~H3 Lysine 4 Demethylating rice Rice JMJ703 in complex with alpha-KG~~	+	[[Category: Chen, X S.]]
		+	[[Category: Lou, Z Y.]]
		+	[[Category: Wang, Q.]]
		+	[[Category: Zhang, F B.]]
		+	[[Category: Zhang, Q F.]]
		+	[[Category: Zhou, D X.]]
		+	[[Category: Histone demethylase]]
		+	[[Category: Jumonjic]]
		+	[[Category: Structural protein]]

OCA at 11:10, 23 January 2013

2013-01-23T11:10:13Z

←Older revision		Revision as of 11:10, 23 January 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4igo is ON HOLD	+	The entry 4igo is ON HOLD until Paper Publication

	Authors: Chen, Q.F., Chen, X.S., Wang, Q., Zhang, F.B., Lou, Z.Y., Zhang, Q.F., Zhou, D.X.		Authors: Chen, Q.F., Chen, X.S., Wang, Q., Zhang, F.B., Lou, Z.Y., Zhang, Q.F., Zhou, D.X.

	Description: Histone H3 Lysine 4 Demethylating rice Rice JMJ703 in complex with alpha-KG		Description: Histone H3 Lysine 4 Demethylating rice Rice JMJ703 in complex with alpha-KG

OCA: Protected "4igo" [edit=sysop:move=sysop]

2013-01-02T08:57:46Z

Protected "4igo" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:57, 2 January 2013

OCA: New page: '''Unreleased structure''' The entry 4igo is ON HOLD Authors: Chen, Q.F., Chen, X.S., Wang, Q., Zhang, F.B., Lou, Z.Y., Zhang, Q.F., Zhou, D.X. Description: Histone H3 Lysine 4 Demethy...

2013-01-02T08:57:45Z

New page: '''Unreleased structure''' The entry 4igo is ON HOLD Authors: Chen, Q.F., Chen, X.S., Wang, Q., Zhang, F.B., Lou, Z.Y., Zhang, Q.F., Zhou, D.X. Description: Histone H3 Lysine 4 Demethy...

New page

'''Unreleased structure'''

The entry 4igo is ON HOLD

Authors: Chen, Q.F., Chen, X.S., Wang, Q., Zhang, F.B., Lou, Z.Y., Zhang, Q.F., Zhou, D.X.

Description: Histone H3 Lysine 4 Demethylating rice Rice JMJ703 in complex with alpha-KG