5nm9 - Revision history

OCA at 13:07, 15 November 2023

OCA — Wed, 15 Nov 2023 13:07:12 GMT

←Older revision		Revision as of 13:07, 15 November 2023
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	==Crystal structure of the placozoa Trichoplax adhaerens Smad4-MH1 bound to the GGCGC site.==		==Crystal structure of the placozoa Trichoplax adhaerens Smad4-MH1 bound to the GGCGC site.==
-	<StructureSection load='5nm9' size='340' side='right' caption='[[5nm9]], [[Resolution\|resolution]] 2.43Å' scene=''>	+	<StructureSection load='5nm9' size='340' side='right'caption='[[5nm9]], [[Resolution\|resolution]] 2.43Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nm9]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Triad Triad~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NM9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NM9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nm9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Trichoplax_adhaerens Trichoplax adhaerens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NM9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NM9 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='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.43Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5mf0\|5mf0]]~~, [[~~5mez~~\|~~5mez]], [[5mey\|5mey~~]]</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">~~TRIADDRAFT_30731 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=10228 TRIAD])~~</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=5nm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nm9 OCA], [https://pdbe.org/5nm9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nm9 RCSB], [https://www.ebi.ac.uk/pdbsum/5nm9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nm9 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=5nm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nm9 OCA], [~~http~~://pdbe.org/5nm9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5nm9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5nm9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5nm9 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B3S7S5_TRIAD B3S7S5_TRIAD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Triad~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Freier, R~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kaczmarska, Z~~]]	+	[[Category: Trichoplax adhaerens]]
-	[[Category: ~~Macias, M J~~]]	+	[[Category: Freier R]]
-	[[Category: ~~Marquez, J A~~]]	+	[[Category: Kaczmarska Z]]
-	[[Category: ~~Dna complex~~]]	+	[[Category: Macias MJ]]
-	[[Category: ~~Smad]]~~	+	[[Category: Marquez JA]]
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription factor~~]]	+

OCA at 08:51, 27 December 2017

OCA — Wed, 27 Dec 2017 08:51:54 GMT

←Older revision		Revision as of 08:51, 27 December 2017
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	<StructureSection load='5nm9' size='340' side='right' caption='[[5nm9]], [[Resolution\|resolution]] 2.43Å' scene=''>		<StructureSection load='5nm9' size='340' side='right' caption='[[5nm9]], [[Resolution\|resolution]] 2.43Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nm9]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NM9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NM9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nm9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Triad Triad]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NM9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NM9 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"><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">[[5mf0\|5mf0]], [[5mez\|5mez]], [[5mey\|5mey]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5mf0\|5mf0]], [[5mez\|5mez]], [[5mey\|5mey]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TRIADDRAFT_30731 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10228 TRIAD])</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=5nm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nm9 OCA], [http://pdbe.org/5nm9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nm9 RCSB], [http://www.ebi.ac.uk/pdbsum/5nm9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nm9 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=5nm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nm9 OCA], [http://pdbe.org/5nm9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nm9 RCSB], [http://www.ebi.ac.uk/pdbsum/5nm9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nm9 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Smad transcription factors activated by TGF-beta or by BMP receptors form trimeric complexes with Smad4 to target specific genes for cell fate regulation. The CAGAC motif has been considered as the main binding element for Smad2/3/4, whereas Smad1/5/8 have been thought to preferentially bind GC-rich elements. However, chromatin immunoprecipitation analysis in embryonic stem cells showed extensive binding of Smad2/3/4 to GC-rich cis-regulatory elements. Here, we present the structural basis for specific binding of Smad3 and Smad4 to GC-rich motifs in the goosecoid promoter, a nodal-regulated differentiation gene. The structures revealed a 5-bp consensus sequence GGC(GC)\|(CG) as the binding site for both TGF-beta and BMP-activated Smads and for Smad4. These 5GC motifs are highly represented as clusters in Smad-bound regions genome-wide. Our results provide a basis for understanding the functional adaptability of Smads in different cellular contexts, and their dependence on lineage-determining transcription factors to target specific genes in TGF-beta and BMP pathways.
		+
		+	Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors.,Martin-Malpartida P, Batet M, Kaczmarska Z, Freier R, Gomes T, Aragon E, Zou Y, Wang Q, Xi Q, Ruiz L, Vea A, Marquez JA, Massague J, Macias MJ Nat Commun. 2017 Dec 12;8(1):2070. doi: 10.1038/s41467-017-02054-6. PMID:29234012<ref>PMID:29234012</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5nm9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Triad]]
	[[Category: Freier, R]]		[[Category: Freier, R]]
	[[Category: Kaczmarska, Z]]		[[Category: Kaczmarska, Z]]

OCA at 07:27, 15 November 2017

OCA — Wed, 15 Nov 2017 07:27:44 GMT

←Older revision		Revision as of 07:27, 15 November 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5nm9 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of the placozoa Trichoplax adhaerens Smad4-MH1 bound to the GGCGC site.==
-		+	<StructureSection load='5nm9' size='340' side='right' caption='[[5nm9]], [[Resolution\|resolution]] 2.43Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5nm9]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NM9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NM9 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">[[5mf0\|5mf0]], [[5mez\|5mez]], [[5mey\|5mey]]</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=5nm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nm9 OCA], [http://pdbe.org/5nm9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nm9 RCSB], [http://www.ebi.ac.uk/pdbsum/5nm9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nm9 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Freier, R]]
		+	[[Category: Kaczmarska, Z]]
		+	[[Category: Macias, M J]]
		+	[[Category: Marquez, J A]]
		+	[[Category: Dna complex]]
		+	[[Category: Smad]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription factor]]

OCA at 09:27, 4 May 2017

OCA — Thu, 04 May 2017 09:27:58 GMT

←Older revision		Revision as of 09:27, 4 May 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5nm9 is ON HOLD	+	The entry 5nm9 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5nm9" [edit=sysop:move=sysop]

OCA — Wed, 12 Apr 2017 08:10:52 GMT

Protected "5nm9" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:10, 12 April 2017

OCA: New page: '''Unreleased structure''' The entry 5nm9 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 12 Apr 2017 08:10:51 GMT

New page: '''Unreleased structure''' The entry 5nm9 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5nm9 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]