6a59 - Revision history

OCA at 09:18, 22 November 2023

2023-11-22T09:18:47Z

←Older revision		Revision as of 09:18, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6a59' size='340' side='right'caption='[[6a59]], [[Resolution\|resolution]] 1.82Å' scene=''>		<StructureSection load='6a59' size='340' side='right'caption='[[6a59]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6a59]] 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=6A59 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6A59 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6a59]] 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=6A59 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A59 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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]] 1.82Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[6a58\|6a58]], [[6a57\|6a57]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">REF6, JMJ12, PKDM9A, At3g48430, T29H11_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'>[https://proteopedia.org/fgij/fg.htm?mol=6a59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a59 OCA], [https://pdbe.org/6a59 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a59 RCSB], [https://www.ebi.ac.uk/pdbsum/6a59 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a59 ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6a59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a59 OCA], [~~http~~://pdbe.org/6a59 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6a59 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6a59 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6a59 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/REF6_ARATH REF6_ARATH]] Histone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3. Demethylates both tri- (H3K27me3) and di-methylated (H3K27me2) H3K27me (PubMed:21642989, PubMed:27111035). Demethylates also H3K4me3/2 and H3K36me3/2 in an in vitro assay (PubMed:20711170). Involved in the transcriptional regulation of hundreds of genes regulating developmental patterning and responses to various stimuli (PubMed:18467490). Binds DNA via its four zinc fingers in a sequence-specific manner, 5'-CTCTGYTY-3', to promote the demethylation of H3K27me3 and the regulation of organ boundary formation (PubMed:27111034, PubMed:27111035). Involved in the regulation of flowering time by repressing FLOWERING LOCUS C (FLC) expression (PubMed:15377760). Interacts with the NF-Y complexe to regulate SOC1 (PubMed:25105952). Mediates the recruitment of BRM to its target loci (PubMed:27111034).<ref>PMID:15377760</ref> <ref>PMID:18467490</ref> <ref>PMID:20711170</ref> <ref>PMID:21642989</ref> <ref>PMID:25105952</ref> <ref>PMID:27111034</ref> <ref>PMID:27111035</ref>	+	[https://www.uniprot.org/uniprot/REF6_ARATH REF6_ARATH] Histone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3. Demethylates both tri- (H3K27me3) and di-methylated (H3K27me2) H3K27me (PubMed:21642989, PubMed:27111035). Demethylates also H3K4me3/2 and H3K36me3/2 in an in vitro assay (PubMed:20711170). Involved in the transcriptional regulation of hundreds of genes regulating developmental patterning and responses to various stimuli (PubMed:18467490). Binds DNA via its four zinc fingers in a sequence-specific manner, 5'-CTCTGYTY-3', to promote the demethylation of H3K27me3 and the regulation of organ boundary formation (PubMed:27111034, PubMed:27111035). Involved in the regulation of flowering time by repressing FLOWERING LOCUS C (FLC) expression (PubMed:15377760). Interacts with the NF-Y complexe to regulate SOC1 (PubMed:25105952). Mediates the recruitment of BRM to its target loci (PubMed:27111034).<ref>PMID:15377760</ref> <ref>PMID:18467490</ref> <ref>PMID:20711170</ref> <ref>PMID:21642989</ref> <ref>PMID:25105952</ref> <ref>PMID:27111034</ref> <ref>PMID:27111035</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arath~~]]	+	[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen, Z]]	+	[[Category: Chen Z]]
-	[[Category: Tian, Z]]	+	[[Category: Tian Z]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Histone demethylase ref6]]~~	+
-	~~[[Category: Zinc finger~~]]	+

OCA at 14:27, 8 July 2020

2020-07-08T14:27:19Z

←Older revision		Revision as of 14:27, 8 July 2020
Line 3:		Line 3:
	<StructureSection load='6a59' size='340' side='right'caption='[[6a59]], [[Resolution\|resolution]] 1.82Å' scene=''>		<StructureSection load='6a59' size='340' side='right'caption='[[6a59]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6a59]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A59 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6A59 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6a59]] 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=6A59 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6A59 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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" id="ligandDat"><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">[[6a58\|6a58]], [[6a57\|6a57]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6a58\|6a58]], [[6a57\|6a57]]</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=6a59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a59 OCA], [http://pdbe.org/6a59 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a59 RCSB], [http://www.ebi.ac.uk/pdbsum/6a59 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a59 ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">REF6, JMJ12, PKDM9A, At3g48430, T29H11_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://proteopedia.org/fgij/fg.htm?mol=6a59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a59 OCA], [http://pdbe.org/6a59 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a59 RCSB], [http://www.ebi.ac.uk/pdbsum/6a59 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a59 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/REF6_ARATH REF6_ARATH]] Histone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3. Demethylates both tri- (H3K27me3) and di-methylated (H3K27me2) H3K27me (PubMed:21642989, PubMed:27111035). Demethylates also H3K4me3/2 and H3K36me3/2 in an in vitro assay (PubMed:20711170). Involved in the transcriptional regulation of hundreds of genes regulating developmental patterning and responses to various stimuli (PubMed:18467490). Binds DNA via its four zinc fingers in a sequence-specific manner, 5'-CTCTGYTY-3', to promote the demethylation of H3K27me3 and the regulation of organ boundary formation (PubMed:27111034, PubMed:27111035). Involved in the regulation of flowering time by repressing FLOWERING LOCUS C (FLC) expression (PubMed:15377760). Interacts with the NF-Y complexe to regulate SOC1 (PubMed:25105952). Mediates the recruitment of BRM to its target loci (PubMed:27111034).<ref>PMID:15377760</ref> <ref>PMID:18467490</ref> <ref>PMID:20711170</ref> <ref>PMID:21642989</ref> <ref>PMID:25105952</ref> <ref>PMID:27111034</ref> <ref>PMID:27111035</ref>		[[http://www.uniprot.org/uniprot/REF6_ARATH REF6_ARATH]] Histone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3. Demethylates both tri- (H3K27me3) and di-methylated (H3K27me2) H3K27me (PubMed:21642989, PubMed:27111035). Demethylates also H3K4me3/2 and H3K36me3/2 in an in vitro assay (PubMed:20711170). Involved in the transcriptional regulation of hundreds of genes regulating developmental patterning and responses to various stimuli (PubMed:18467490). Binds DNA via its four zinc fingers in a sequence-specific manner, 5'-CTCTGYTY-3', to promote the demethylation of H3K27me3 and the regulation of organ boundary formation (PubMed:27111034, PubMed:27111035). Involved in the regulation of flowering time by repressing FLOWERING LOCUS C (FLC) expression (PubMed:15377760). Interacts with the NF-Y complexe to regulate SOC1 (PubMed:25105952). Mediates the recruitment of BRM to its target loci (PubMed:27111034).<ref>PMID:15377760</ref> <ref>PMID:18467490</ref> <ref>PMID:20711170</ref> <ref>PMID:21642989</ref> <ref>PMID:25105952</ref> <ref>PMID:27111034</ref> <ref>PMID:27111035</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Relative of Early Flowing 6 (REF6) is a DNA-sequence-specific H3K27me3/2 demethylase that contains four zinc finger (ZnF) domains and targets several thousand genes in Arabidopsis thaliana. The ZnF domains are essential for binding target genes, but the structural basis remains unclear. Here, we determined crystal structures of the ZnF domains and REF6-DNA complex, revealing a unique REF6-family-specific half-cross-braced ZnF (RCZ) domain and two C2H2-type ZnFs. DNA-binding induces a profound conformational change in the hinge region of REF6. Each REF6 recognizes six bases and DNA methylation reduces the binding affinity. Both the acidic region and basic region are important for the self-association of REF6. The REF6 DNA-binding affinity is determined by the sequence-dependent conformations of DNA and also the cooperativity in different target motifs. The conformational plasticity enables REF6 to function as a global transcriptional regulator that directly binds to many diverse genes, revealing the structural basis for the epigenetic modification recognition.
		+
		+	Crystal structures of REF6 and its complex with DNA reveal diverse recognition mechanisms.,Tian Z, Li X, Li M, Wu W, Zhang M, Tang C, Li Z, Liu Y, Chen Z, Yang M, Ma L, Caba C, Tong Y, Lam HM, Dai S, Chen Z Cell Discov. 2020 Mar 31;6:17. doi: 10.1038/s41421-020-0150-6. eCollection 2020. PMID:32257379<ref>PMID:32257379</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6a59" 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: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chen, Z]]		[[Category: Chen, Z]]

OCA at 06:42, 26 June 2019

2019-06-26T06:42:38Z

←Older revision		Revision as of 06:42, 26 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6a59 is ~~ON HOLD until Jun 22 2020~~	+	==Structure of histone demethylase REF6 at 1.8A==
-		+	<StructureSection load='6a59' size='340' side='right'caption='[[6a59]], [[Resolution\|resolution]] 1.82Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6a59]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A59 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A59 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6a58\|6a58]], [[6a57\|6a57]]</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=6a59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a59 OCA], [http://pdbe.org/6a59 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a59 RCSB], [http://www.ebi.ac.uk/pdbsum/6a59 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a59 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/REF6_ARATH REF6_ARATH]] Histone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3. Demethylates both tri- (H3K27me3) and di-methylated (H3K27me2) H3K27me (PubMed:21642989, PubMed:27111035). Demethylates also H3K4me3/2 and H3K36me3/2 in an in vitro assay (PubMed:20711170). Involved in the transcriptional regulation of hundreds of genes regulating developmental patterning and responses to various stimuli (PubMed:18467490). Binds DNA via its four zinc fingers in a sequence-specific manner, 5'-CTCTGYTY-3', to promote the demethylation of H3K27me3 and the regulation of organ boundary formation (PubMed:27111034, PubMed:27111035). Involved in the regulation of flowering time by repressing FLOWERING LOCUS C (FLC) expression (PubMed:15377760). Interacts with the NF-Y complexe to regulate SOC1 (PubMed:25105952). Mediates the recruitment of BRM to its target loci (PubMed:27111034).<ref>PMID:15377760</ref> <ref>PMID:18467490</ref> <ref>PMID:20711170</ref> <ref>PMID:21642989</ref> <ref>PMID:25105952</ref> <ref>PMID:27111034</ref> <ref>PMID:27111035</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chen, Z]]
		+	[[Category: Tian, Z]]
		+	[[Category: Complex]]
		+	[[Category: Dna]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Histone demethylase ref6]]
		+	[[Category: Zinc finger]]

OCA at 03:55, 11 July 2018

2018-07-11T03:55:30Z

←Older revision		Revision as of 03:55, 11 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6a59 is ON HOLD	+	The entry 6a59 is ON HOLD until Jun 22 2020

	Authors:		Authors:

OCA: Protected "6a59" [edit=sysop:move=sysop]

2018-06-27T03:56:15Z

Protected "6a59" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:56, 27 June 2018

OCA: New page: '''Unreleased structure''' The entry 6a59 is ON HOLD Authors: Description: Category: Unreleased Structures

2018-06-27T03:56:14Z

New page: '''Unreleased structure''' The entry 6a59 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6a59 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]