5nvo - Revision history

OCA at 12:10, 22 November 2023

OCA — Wed, 22 Nov 2023 12:10:36 GMT

←Older revision		Revision as of 12:10, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5nvo' size='340' side='right'caption='[[5nvo]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5nvo' size='340' side='right'caption='[[5nvo]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nvo]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NVO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NVO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nvo]] 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=5NVO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NVO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CHT:CHOLINE+ION'>CHT</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]] 2.4Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>DNMT3B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CHT:CHOLINE+ION'>CHT</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5nvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nvo OCA], [https://pdbe.org/5nvo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nvo RCSB], [https://www.ebi.ac.uk/pdbsum/5nvo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nvo 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=5nvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nvo OCA], [~~http~~://pdbe.org/5nvo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5nvo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5nvo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5nvo 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 20:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[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 06:48, 16 October 2019

OCA — Wed, 16 Oct 2019 06:48:49 GMT

←Older revision		Revision as of 06:48, 16 October 2019
Line 1:		Line 1:

	==Human DNMT3B PWWP domain in complex with choline==		==Human DNMT3B PWWP domain in complex with choline==
-	<StructureSection load='5nvo' size='340' side='right' caption='[[5nvo]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='5nvo' size='340' side='right'caption='[[5nvo]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nvo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NVO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NVO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nvo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NVO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NVO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CHT:CHOLINE+ION'>CHT</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"><scene name='pdbligand=CHT:CHOLINE+ION'>CHT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DNMT3B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5nvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nvo OCA], [http://pdbe.org/5nvo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nvo RCSB], [http://www.ebi.ac.uk/pdbsum/5nvo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nvo 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=5nvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nvo OCA], [http://pdbe.org/5nvo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nvo RCSB], [http://www.ebi.ac.uk/pdbsum/5nvo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nvo ProSAT]</span></td></tr>
Line 12:		Line 13:
	== 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: Human]]
		+	[[Category: Large Structures]]
	[[Category: Rondelet, G]]		[[Category: Rondelet, G]]
	[[Category: Wouters, J]]		[[Category: Wouters, J]]

OCA at 05:25, 30 May 2018

OCA — Wed, 30 May 2018 05:25:02 GMT

←Older revision		Revision as of 05:25, 30 May 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5nvo is ~~ON HOLD~~	+	==Human DNMT3B PWWP domain in complex with choline==
-		+	<StructureSection load='5nvo' size='340' side='right' caption='[[5nvo]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~Authors~~: ~~Rondelet~~, G., ~~Wouters~~, J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5nvo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NVO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NVO FirstGlance]. <br>
-	~~Description~~: ~~Human DNMT3B PWWP domain~~ in ~~complex~~ with ~~choline~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CHT:CHOLINE+ION'>CHT</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=5nvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nvo OCA], [http://pdbe.org/5nvo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nvo RCSB], [http://www.ebi.ac.uk/pdbsum/5nvo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nvo 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: Protected "5nvo" [edit=sysop:move=sysop]

OCA — Wed, 10 May 2017 09:28:04 GMT

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

←Older revision

Revision as of 09:28, 10 May 2017

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

OCA — Wed, 10 May 2017 09:28:03 GMT

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

New page

'''Unreleased structure'''

The entry 5nvo is ON HOLD

Authors: Rondelet, G., Wouters, J.

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