5lty - Revision history

OCA at 18:49, 18 October 2023

OCA — Wed, 18 Oct 2023 18:49:22 GMT

←Older revision		Revision as of 18:49, 18 October 2023
Line 1:		Line 1:

	==Homeobox transcription factor CDX2 bound to methylated DNA==		==Homeobox transcription factor CDX2 bound to methylated DNA==
-	<StructureSection load='5lty' size='340' side='right' caption='[[5lty]], [[Resolution\|resolution]] 2.66Å' scene=''>	+	<StructureSection load='5lty' size='340' side='right'caption='[[5lty]], [[Resolution\|resolution]] 2.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lty]] is a 6 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=5LTY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5LTY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lty]] is a 6 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=5LTY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LTY FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.66Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~CDX2, CDX3 ([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=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=5lty FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lty OCA], [~~http~~://pdbe.org/5lty PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5lty RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5lty PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5lty 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=5lty FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lty OCA], [https://pdbe.org/5lty PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lty RCSB], [https://www.ebi.ac.uk/pdbsum/5lty PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lty ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CDX2_HUMAN CDX2_HUMAN]] Involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium. Important in broad range of functions from early differentiation to maintenance of the intestinal epithelial lining of both the small and large intestine.	+	[https://www.uniprot.org/uniprot/CDX2_HUMAN CDX2_HUMAN] Involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium. Important in broad range of functions from early differentiation to maintenance of the intestinal epithelial lining of both the small and large intestine.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Morgunova, E~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Popov, A~~]]	+	[[Category: Morgunova E]]
-	[[Category: ~~Taipale, J~~]]	+	[[Category: Popov A]]
-	[[Category: ~~Methylated dna]]~~	+	[[Category: Taipale J]]
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription factor~~]]	+

OCA at 11:40, 16 November 2017

OCA — Thu, 16 Nov 2017 11:40:10 GMT

←Older revision		Revision as of 11:40, 16 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5lty is ~~ON HOLD until Paper~~ Publication	+	==Homeobox transcription factor CDX2 bound to methylated DNA==
		+	<StructureSection load='5lty' size='340' side='right' caption='[[5lty]], [[Resolution\|resolution]] 2.66Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5lty]] is a 6 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=5LTY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LTY FirstGlance]. <br>
		+	</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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CDX2, CDX3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5lty FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lty OCA], [http://pdbe.org/5lty PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lty RCSB], [http://www.ebi.ac.uk/pdbsum/5lty PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lty ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CDX2_HUMAN CDX2_HUMAN]] Involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium. Important in broad range of functions from early differentiation to maintenance of the intestinal epithelial lining of both the small and large intestine.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The majority of CpG dinucleotides in the human genome are methylated at cytosine bases. However, active gene regulatory elements are generally hypomethylated relative to their flanking regions, and the binding of some transcription factors (TFs) is diminished by methylation of their target sequences. By analysis of 542 human TFs with methylation-sensitive SELEX (systematic evolution of ligands by exponential enrichment), we found that there are also many TFs that prefer CpG-methylated sequences. Most of these are in the extended homeodomain family. Structural analysis showed that homeodomain specificity for methylcytosine depends on direct hydrophobic interactions with the methylcytosine 5-methyl group. This study provides a systematic examination of the effect of an epigenetic DNA modification on human TF binding specificity and reveals that many developmentally important proteins display preference for mCpG-containing sequences.

-	~~Authors~~:	+	Impact of cytosine methylation on DNA binding specificities of human transcription factors.,Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schubeler D, Vinson C, Taipale J Science. 2017 May 5;356(6337). pii: eaaj2239. doi: 10.1126/science.aaj2239. PMID:28473536<ref>PMID:28473536</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5lty" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Morgunova, E]]
		+	[[Category: Popov, A]]
		+	[[Category: Taipale, J]]
		+	[[Category: Methylated dna]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription factor]]

OCA at 11:49, 21 September 2016

OCA — Wed, 21 Sep 2016 11:49:12 GMT

←Older revision		Revision as of 11:49, 21 September 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 14 Sep 2016 13:41:28 GMT

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

←Older revision

Revision as of 13:41, 14 September 2016

OCA: New page: '''Unreleased structure''' The entry 5lty is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 14 Sep 2016 13:41:26 GMT

New page: '''Unreleased structure''' The entry 5lty is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5lty is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]