5nr3 - Revision history

OCA at 12:03, 22 November 2023

OCA — Wed, 22 Nov 2023 12:03:19 GMT

←Older revision		Revision as of 12:03, 22 November 2023
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	<StructureSection load='5nr3' size='340' side='right'caption='[[5nr3]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5nr3' size='340' side='right'caption='[[5nr3]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nr3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NR3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5NR3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nr3]] is a 2 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=5NR3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NR3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=95E:Ethambutol'>95E</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http:~~/~~/en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase]~~, ~~with EC number [http~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=95E:Ethambutol'>95E</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5nr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nr3 OCA], [~~http~~://pdbe.org/5nr3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5nr3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5nr3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5nr3 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=5nr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nr3 OCA], [https://pdbe.org/5nr3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nr3 RCSB], [https://www.ebi.ac.uk/pdbsum/5nr3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nr3 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/DNM3B_HUMAN DNM3B_HUMAN]] ICF syndrome. The disease is caused by mutations affecting the gene represented in this entry.<ref>PMID:10647011</ref> <ref>PMID:10555141</ref> <ref>PMID:10588719</ref> <ref>PMID:11102980</ref> <ref>PMID:15580563</ref>	+	[https://www.uniprot.org/uniprot/DNM3B_HUMAN DNM3B_HUMAN] ICF syndrome. The disease is caused by mutations affecting the gene represented in this entry.<ref>PMID:10647011</ref> <ref>PMID:10555141</ref> <ref>PMID:10588719</ref> <ref>PMID:11102980</ref> <ref>PMID:15580563</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DNM3B_HUMAN DNM3B_HUMAN]] Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. May preferentially methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing (By similarity). In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Isoforms 4 and 5 are probably not functional due to the deletion of two conserved methyltransferase motifs. Function as transcriptional corepressor by associating with ZHX1.<ref>PMID:16357870</ref> <ref>PMID:17303076</ref> <ref>PMID:18413740</ref> <ref>PMID:18567530</ref>	+	[https://www.uniprot.org/uniprot/DNM3B_HUMAN DNM3B_HUMAN] Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. May preferentially methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing (By similarity). In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Isoforms 4 and 5 are probably not functional due to the deletion of two conserved methyltransferase motifs. Function as transcriptional corepressor by associating with ZHX1.<ref>PMID:16357870</ref> <ref>PMID:17303076</ref> <ref>PMID:18413740</ref> <ref>PMID:18567530</ref>

	==See Also==		==See Also==
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Rondelet, G]]	+	[[Category: Rondelet G]]
-	[[Category: Wouters, J]]	+	[[Category: Wouters J]]
-	~~[[Category: Beta barrel]]~~	+
-	~~[[Category: Dnmt3b pwwp domain]]~~	+
-	~~[[Category: Histone binding]]~~	+
-	~~[[Category: Ligand]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 12:10, 26 August 2020

OCA — Wed, 26 Aug 2020 12:10:41 GMT

←Older revision		Revision as of 12:10, 26 August 2020
Line 1:		Line 1:

	==Human DNMT3B PWWP domain in complex with ethambutol==		==Human DNMT3B PWWP domain in complex with ethambutol==
-	<StructureSection load='5nr3' size='340' side='right' caption='[[5nr3]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5nr3' size='340' side='right'caption='[[5nr3]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nr3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NR3 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NR3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nr3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NR3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5NR3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=95E:Ethambutol'>95E</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=95E:Ethambutol'>95E</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37] </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=5nr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nr3 OCA], [http://pdbe.org/5nr3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nr3 RCSB], [http://www.ebi.ac.uk/pdbsum/5nr3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nr3 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=5nr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nr3 OCA], [http://pdbe.org/5nr3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nr3 RCSB], [http://www.ebi.ac.uk/pdbsum/5nr3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nr3 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 12:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/DNM3B_HUMAN DNM3B_HUMAN]] Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. May preferentially methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing (By similarity). In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Isoforms 4 and 5 are probably not functional due to the deletion of two conserved methyltransferase motifs. Function as transcriptional corepressor by associating with ZHX1.<ref>PMID:16357870</ref> <ref>PMID:17303076</ref> <ref>PMID:18413740</ref> <ref>PMID:18567530</ref>		[[http://www.uniprot.org/uniprot/DNM3B_HUMAN DNM3B_HUMAN]] Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. May preferentially methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing (By similarity). In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Isoforms 4 and 5 are probably not functional due to the deletion of two conserved methyltransferase motifs. Function as transcriptional corepressor by associating with ZHX1.<ref>PMID:16357870</ref> <ref>PMID:17303076</ref> <ref>PMID:18413740</ref> <ref>PMID:18567530</ref>
		+
		+	==See Also==
		+	*[[DNA methyltransferase 3D structures\|DNA methyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Rondelet, G]]		[[Category: Rondelet, G]]
	[[Category: Wouters, J]]		[[Category: Wouters, J]]

OCA at 05:23, 30 May 2018

OCA — Wed, 30 May 2018 05:23:53 GMT

←Older revision		Revision as of 05:23, 30 May 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5nr3 is ~~ON HOLD until Paper Publication~~	+	==Human DNMT3B PWWP domain in complex with ethambutol==
-		+	<StructureSection load='5nr3' size='340' side='right' caption='[[5nr3]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~Authors~~: ~~Rondelet~~, G., ~~Wouters~~, J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5nr3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NR3 FirstGlance]. <br>
-	~~Description~~: ~~Human DNMT3B PWWP domain~~ in ~~complex~~ with ~~ethambutol~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=95E:Ethambutol'>95E</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37] </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=5nr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nr3 OCA], [http://pdbe.org/5nr3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nr3 RCSB], [http://www.ebi.ac.uk/pdbsum/5nr3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nr3 ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/DNM3B_HUMAN DNM3B_HUMAN]] ICF syndrome. The disease is caused by mutations affecting the gene represented in this entry.<ref>PMID:10647011</ref> <ref>PMID:10555141</ref> <ref>PMID:10588719</ref> <ref>PMID:11102980</ref> <ref>PMID:15580563</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DNM3B_HUMAN DNM3B_HUMAN]] Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. May preferentially methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing (By similarity). In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Isoforms 4 and 5 are probably not functional due to the deletion of two conserved methyltransferase motifs. Function as transcriptional corepressor by associating with ZHX1.<ref>PMID:16357870</ref> <ref>PMID:17303076</ref> <ref>PMID:18413740</ref> <ref>PMID:18567530</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Rondelet, G]]
	[[Category: Wouters, J]]		[[Category: Wouters, J]]
-	[[Category: ~~Rondelet, G~~]]	+	[[Category: Beta barrel]]
		+	[[Category: Dnmt3b pwwp domain]]
		+	[[Category: Histone binding]]
		+	[[Category: Ligand]]
		+	[[Category: Transferase]]

OCA at 09:15, 10 May 2017

OCA — Wed, 10 May 2017 09:15:36 GMT

←Older revision		Revision as of 09:15, 10 May 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5nr3 is ON HOLD	+	The entry 5nr3 is ON HOLD until Paper Publication

	Authors: Rondelet, G., Wouters, J.		Authors: Rondelet, G., Wouters, J.

OCA: Protected "5nr3" [edit=sysop:move=sysop]

OCA — Thu, 04 May 2017 09:36:22 GMT

Protected "5nr3" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:36, 4 May 2017

OCA: New page: '''Unreleased structure''' The entry 5nr3 is ON HOLD Authors: Rondelet, G., Wouters, J. Description: Human DNMT3B PWWP domain in complex with ethambutol [[Category: Unreleased Structur...

OCA — Thu, 04 May 2017 09:36:20 GMT

New page: '''Unreleased structure''' The entry 5nr3 is ON HOLD Authors: Rondelet, G., Wouters, J. Description: Human DNMT3B PWWP domain in complex with ethambutol [[Category: Unreleased Structur...

New page

'''Unreleased structure'''

The entry 5nr3 is ON HOLD

Authors: Rondelet, G., Wouters, J.

Description: Human DNMT3B PWWP domain in complex with ethambutol
[[Category: Unreleased Structures]]
[[Category: Wouters, J]]
[[Category: Rondelet, G]]