6d1t - Revision history

OCA at 15:16, 4 October 2023

2023-10-04T15:16:03Z

←Older revision		Revision as of 15:16, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='6d1t' size='340' side='right'caption='[[6d1t]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='6d1t' size='340' side='right'caption='[[6d1t]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6d1t]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D1T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6D1T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6d1t]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D1T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6D1T FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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]] 2.25Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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=6d1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d1t OCA], [~~http~~://pdbe.org/6d1t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6d1t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6d1t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6d1t 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=6d1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d1t OCA], [https://pdbe.org/6d1t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d1t RCSB], [https://www.ebi.ac.uk/pdbsum/6d1t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d1t ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MBD1_HUMAN MBD1_HUMAN]] Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Isoform 1 and isoform 2 can also repress transcription from unmethylated promoters.<ref>PMID:9207790</ref> <ref>PMID:10454587</ref> <ref>PMID:9774669</ref> <ref>PMID:10648624</ref> <ref>PMID:12711603</ref> <ref>PMID:12665582</ref> <ref>PMID:12697822</ref> <ref>PMID:14610093</ref> <ref>PMID:15327775</ref> <ref>PMID:14555760</ref>	+	[https://www.uniprot.org/uniprot/MBD1_HUMAN MBD1_HUMAN] Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Isoform 1 and isoform 2 can also repress transcription from unmethylated promoters.<ref>PMID:9207790</ref> <ref>PMID:10454587</ref> <ref>PMID:9774669</ref> <ref>PMID:10648624</ref> <ref>PMID:12711603</ref> <ref>PMID:12665582</ref> <ref>PMID:12697822</ref> <ref>PMID:14610093</ref> <ref>PMID:15327775</ref> <ref>PMID:14555760</ref>

	==See Also==		==See Also==
Line 17:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arrowsmith~~, C H~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Bountra, C]]	+	[[Category: Arrowsmith CH]]
-	[[Category: Edwards~~, A M~~]]	+	[[Category: Bountra C]]
-	[[Category: Liu, K]]	+	[[Category: Edwards AM]]
-	[[Category: Min, J]]	+	[[Category: Liu K]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Min J]]
-	[[Category: Tempel, W]]	+	[[Category: Tempel W]]
-	[[Category: Xu, C]]	+	[[Category: Xu C]]
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Dna-methylation]]~~	+
-	~~[[Category: Mbd]]~~	+
-	~~[[Category: Sgc~~]]	+

OCA at 09:03, 11 November 2020

2020-11-11T09:03:12Z

←Older revision		Revision as of 09:03, 11 November 2020
Line 1:		Line 1:

	==Complex of MBD1-MBD and methylated DNA==		==Complex of MBD1-MBD and methylated DNA==
-	<StructureSection load='6d1t' size='340' side='right' caption='[[6d1t]], [[Resolution\|resolution]] 2.25Å' scene=''>	+	<StructureSection load='6d1t' size='340' side='right'caption='[[6d1t]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6d1t]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D1T OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6D1T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6d1t]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D1T OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6D1T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</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=6d1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d1t OCA], [http://pdbe.org/6d1t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d1t RCSB], [http://www.ebi.ac.uk/pdbsum/6d1t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d1t 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=6d1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d1t OCA], [http://pdbe.org/6d1t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d1t RCSB], [http://www.ebi.ac.uk/pdbsum/6d1t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d1t ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/MBD1_HUMAN MBD1_HUMAN]] Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Isoform 1 and isoform 2 can also repress transcription from unmethylated promoters.<ref>PMID:9207790</ref> <ref>PMID:10454587</ref> <ref>PMID:9774669</ref> <ref>PMID:10648624</ref> <ref>PMID:12711603</ref> <ref>PMID:12665582</ref> <ref>PMID:12697822</ref> <ref>PMID:14610093</ref> <ref>PMID:15327775</ref> <ref>PMID:14555760</ref>		[[http://www.uniprot.org/uniprot/MBD1_HUMAN MBD1_HUMAN]] Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Isoform 1 and isoform 2 can also repress transcription from unmethylated promoters.<ref>PMID:9207790</ref> <ref>PMID:10454587</ref> <ref>PMID:9774669</ref> <ref>PMID:10648624</ref> <ref>PMID:12711603</ref> <ref>PMID:12665582</ref> <ref>PMID:12697822</ref> <ref>PMID:14610093</ref> <ref>PMID:15327775</ref> <ref>PMID:14555760</ref>
		+
		+	==See Also==
		+	*[[Methyl CpG binding protein 3D structures\|Methyl CpG binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Bountra, C]]		[[Category: Bountra, C]]

OCA at 06:19, 9 May 2018

2018-05-09T06:19:34Z

←Older revision		Revision as of 06:19, 9 May 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6d1t is ~~ON HOLD~~	+	==Complex of MBD1-MBD and methylated DNA==
-		+	<StructureSection load='6d1t' size='340' side='right' caption='[[6d1t]], [[Resolution\|resolution]] 2.25Å' scene=''>
-	~~Authors~~: ~~Liu, K~~.~~, Xu, C~~.~~, Tempel, W~~., ~~Arrowsmith, C~~.H.~~, Bountra, C~~., ~~Edwards~~, A.M., ~~Min, J~~., ~~Structural Genomics Consortium (SGC)~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6d1t]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D1T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D1T FirstGlance]. <br>
-	~~Description~~: ~~Complex~~ of ~~MBD1~~-~~MBD~~ and ~~methylated~~ DNA	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>
-	[[Category: ~~Arrowsmith~~, C.H]]	+	<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=6d1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d1t OCA], [http://pdbe.org/6d1t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d1t RCSB], [http://www.ebi.ac.uk/pdbsum/6d1t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d1t ProSAT]</span></td></tr>
-	[[Category: Xu, C]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MBD1_HUMAN MBD1_HUMAN]] Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Isoform 1 and isoform 2 can also repress transcription from unmethylated promoters.<ref>PMID:9207790</ref> <ref>PMID:10454587</ref> <ref>PMID:9774669</ref> <ref>PMID:10648624</ref> <ref>PMID:12711603</ref> <ref>PMID:12665582</ref> <ref>PMID:12697822</ref> <ref>PMID:14610093</ref> <ref>PMID:15327775</ref> <ref>PMID:14555760</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arrowsmith, C H]]
		+	[[Category: Bountra, C]]
		+	[[Category: Edwards, A M]]
	[[Category: Liu, K]]		[[Category: Liu, K]]
	[[Category: Min, J]]		[[Category: Min, J]]
-	~~[[Category: Edwards, A.M]]~~	+	[[Category: Structural genomic]]
-	[[Category: Structural ~~Genomics Consortium (Sgc)]]~~	+
-	~~[[Category: Bountra, C~~]]	+
	[[Category: Tempel, W]]		[[Category: Tempel, W]]
		+	[[Category: Xu, C]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Dna-methylation]]
		+	[[Category: Mbd]]
		+	[[Category: Sgc]]

OCA: Protected "6d1t" [edit=sysop:move=sysop]

2018-04-18T04:21:58Z

Protected "6d1t" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:21, 18 April 2018

OCA: New page: '''Unreleased structure''' The entry 6d1t is ON HOLD Authors: Liu, K., Xu, C., Tempel, W., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC) D...

2018-04-18T04:21:56Z

New page: '''Unreleased structure''' The entry 6d1t is ON HOLD Authors: Liu, K., Xu, C., Tempel, W., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC) D...

New page

'''Unreleased structure'''

The entry 6d1t is ON HOLD

Authors: Liu, K., Xu, C., Tempel, W., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Description: Complex of MBD1-MBD and methylated DNA
[[Category: Unreleased Structures]]
[[Category: Arrowsmith, C.H]]
[[Category: Xu, C]]
[[Category: Liu, K]]
[[Category: Min, J]]
[[Category: Edwards, A.M]]
[[Category: Structural Genomics Consortium (Sgc)]]
[[Category: Bountra, C]]
[[Category: Tempel, W]]