4ov7 - Revision history

OCA at 12:42, 1 March 2024

OCA — Fri, 01 Mar 2024 12:42:03 GMT

←Older revision		Revision as of 12:42, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ov7]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OV7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OV7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ov7]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OV7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OV7 FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.701Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ov7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ov7 OCA], [https://pdbe.org/4ov7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ov7 RCSB], [https://www.ebi.ac.uk/pdbsum/4ov7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ov7 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=4ov7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ov7 OCA], [https://pdbe.org/4ov7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ov7 RCSB], [https://www.ebi.ac.uk/pdbsum/4ov7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ov7 ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Complex gene regulatory networks require transcription factors (TFs) to bind distinct DNA sequences. To understand how novel TF specificity evolves, we combined phylogenetic, biochemical, and biophysical approaches to interrogate how DNA recognition diversified in the steroid hormone receptor (SR) family. After duplication of the ancestral SR, three mutations in one copy radically weakened binding to the ancestral estrogen response element (ERE) and improved binding to a new set of DNA sequences (steroid response elements, SREs). They did so by establishing unfavorable interactions with ERE and abolishing unfavorable interactions with SRE; also required were numerous permissive substitutions, which nonspecifically improved cooperativity and affinity of DNA binding. Our findings indicate that negative determinants of binding play key roles in TFs' DNA selectivity and-with our prior work on the evolution of SR ligand specificity during the same interval-show how a specific new gene regulatory module evolved without interfering with the integrity of the ancestral module.
-
-	Evolution of DNA specificity in a transcription factor family produced a new gene regulatory module.,McKeown AN, Bridgham JT, Anderson DW, Murphy MN, Ortlund EA, Thornton JW Cell. 2014 Sep 25;159(1):58-68. doi: 10.1016/j.cell.2014.09.003. PMID:25259920<ref>PMID:25259920</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4ov7" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:47, 25 January 2023

OCA — Wed, 25 Jan 2023 07:47:30 GMT

←Older revision		Revision as of 07:47, 25 January 2023
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	<StructureSection load='4ov7' size='340' side='right'caption='[[4ov7]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='4ov7' size='340' side='right'caption='[[4ov7]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ov7]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OV7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4OV7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ov7]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OV7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OV7 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" id="ligandDat"><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">[[4ond\|4ond]], [[4oln\|4oln]], [[4oor\|4oor]]~~</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=4ov7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ov7 OCA], [https://pdbe.org/4ov7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ov7 RCSB], [https://www.ebi.ac.uk/pdbsum/4ov7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ov7 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=4ov7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ov7 OCA], [~~http~~://pdbe.org/4ov7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ov7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ov7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ov7 ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Ortlund~~, E A]]~~	+	[[Category: Ortlund EA]]
-	~~[[Category: Steroid receptor dna binding domain]]~~	+
-	~~[[Category: Transcription factor]]~~	+
-	~~[[Category: Transcription-dna complex]]~~	+
-	~~[[Category: Zinc finger~~]]	+

OCA at 08:07, 19 February 2020

OCA — Wed, 19 Feb 2020 08:07:02 GMT

←Older revision		Revision as of 08:07, 19 February 2020
Line 1:		Line 1:

	==Ancestral Steroid Receptor 2 DBD helix mutant - SRE DNA complex==		==Ancestral Steroid Receptor 2 DBD helix mutant - SRE DNA complex==
-	<StructureSection load='4ov7' size='340' side='right' caption='[[4ov7]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='4ov7' size='340' side='right'caption='[[4ov7]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ov7]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OV7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OV7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ov7]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OV7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OV7 FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Synthetic construct sequences]]		[[Category: Synthetic construct sequences]]
	[[Category: Ortlund, E A]]		[[Category: Ortlund, E A]]

OCA at 08:30, 22 November 2017

OCA — Wed, 22 Nov 2017 08:30:48 GMT

←Older revision		Revision as of 08:30, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='4ov7' size='340' side='right' caption='[[4ov7]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='4ov7' size='340' side='right' caption='[[4ov7]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ov7]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OV7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OV7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ov7]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OV7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OV7 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">[[4ond\|4ond]], [[4oln\|4oln]], [[4oor\|4oor]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ond\|4ond]], [[4oln\|4oln]], [[4oor\|4oor]]</td></tr>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Synthetic construct sequences]]
	[[Category: Ortlund, E A]]		[[Category: Ortlund, E A]]
	[[Category: Steroid receptor dna binding domain]]		[[Category: Steroid receptor dna binding domain]]

OCA at 09:24, 11 August 2016

OCA — Thu, 11 Aug 2016 09:24:39 GMT

←Older revision		Revision as of 09:24, 11 August 2016
Line 1:		Line 1:
		+
	==Ancestral Steroid Receptor 2 DBD helix mutant - SRE DNA complex==		==Ancestral Steroid Receptor 2 DBD helix mutant - SRE DNA complex==
	<StructureSection load='4ov7' size='340' side='right' caption='[[4ov7]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='4ov7' size='340' side='right' caption='[[4ov7]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 5:		Line 6:
	</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">[[4ond\|4ond]], [[4oln\|4oln]], [[4oor\|4oor]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ond\|4ond]], [[4oln\|4oln]], [[4oor\|4oor]]</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=4ov7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ov7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ov7 RCSB], [http://www.ebi.ac.uk/pdbsum/4ov7 PDBsum]</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=4ov7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ov7 OCA], [http://pdbe.org/4ov7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ov7 RCSB], [http://www.ebi.ac.uk/pdbsum/4ov7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ov7 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4ov7" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:27, 25 January 2015

OCA — Sun, 25 Jan 2015 10:27:58 GMT

←Older revision		Revision as of 10:27, 25 January 2015
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Ortlund, E A.]]	+	[[Category: Ortlund, E A]]
	[[Category: Steroid receptor dna binding domain]]		[[Category: Steroid receptor dna binding domain]]
	[[Category: Transcription factor]]		[[Category: Transcription factor]]
	[[Category: Transcription-dna complex]]		[[Category: Transcription-dna complex]]
	[[Category: Zinc finger]]		[[Category: Zinc finger]]

OCA at 11:22, 29 October 2014

OCA — Wed, 29 Oct 2014 11:22:12 GMT

←Older revision		Revision as of 11:22, 29 October 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Ancestral Steroid Receptor 2 DBD helix mutant - SRE DNA complex==
		+	<StructureSection load='4ov7' size='340' side='right' caption='[[4ov7]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ov7]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OV7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OV7 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>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ond\|4ond]], [[4oln\|4oln]], [[4oor\|4oor]]</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=4ov7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ov7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ov7 RCSB], [http://www.ebi.ac.uk/pdbsum/4ov7 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Complex gene regulatory networks require transcription factors (TFs) to bind distinct DNA sequences. To understand how novel TF specificity evolves, we combined phylogenetic, biochemical, and biophysical approaches to interrogate how DNA recognition diversified in the steroid hormone receptor (SR) family. After duplication of the ancestral SR, three mutations in one copy radically weakened binding to the ancestral estrogen response element (ERE) and improved binding to a new set of DNA sequences (steroid response elements, SREs). They did so by establishing unfavorable interactions with ERE and abolishing unfavorable interactions with SRE; also required were numerous permissive substitutions, which nonspecifically improved cooperativity and affinity of DNA binding. Our findings indicate that negative determinants of binding play key roles in TFs' DNA selectivity and-with our prior work on the evolution of SR ligand specificity during the same interval-show how a specific new gene regulatory module evolved without interfering with the integrity of the ancestral module.

-	~~The entry 4ov7 is ON HOLD until Paper Publication~~	+	Evolution of DNA specificity in a transcription factor family produced a new gene regulatory module.,McKeown AN, Bridgham JT, Anderson DW, Murphy MN, Ortlund EA, Thornton JW Cell. 2014 Sep 25;159(1):58-68. doi: 10.1016/j.cell.2014.09.003. PMID:25259920<ref>PMID:25259920</ref>

-	~~Authors~~: Ortlund, E.A.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Ancestral~~ Steroid ~~Receptor 2 DBD helix mutant~~ -~~SRE DNA~~ complex	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ortlund, E A.]]
		+	[[Category: Steroid receptor dna binding domain]]
		+	[[Category: Transcription factor]]
		+	[[Category: Transcription-dna complex]]
		+	[[Category: Zinc finger]]

OCA at 06:21, 30 April 2014

OCA — Wed, 30 Apr 2014 06:21:40 GMT

←Older revision		Revision as of 06:21, 30 April 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ov7 is ON HOLD	+	The entry 4ov7 is ON HOLD until Paper Publication

	Authors: Ortlund, E.A.		Authors: Ortlund, E.A.

	Description: Ancestral Steroid Receptor 2 DBD helix mutant -SRE DNA complex		Description: Ancestral Steroid Receptor 2 DBD helix mutant -SRE DNA complex

OCA: Protected "4ov7" [edit=sysop:move=sysop]

OCA — Mon, 03 Mar 2014 16:53:56 GMT

Protected "4ov7" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:53, 3 March 2014

OCA: New page: '''Unreleased structure''' The entry 4ov7 is ON HOLD Authors: Ortlund, E.A. Description: Ancestral Steroid Receptor 2 DBD helix mutant -SRE DNA complex

OCA — Mon, 03 Mar 2014 16:53:55 GMT

New page: '''Unreleased structure''' The entry 4ov7 is ON HOLD Authors: Ortlund, E.A. Description: Ancestral Steroid Receptor 2 DBD helix mutant -SRE DNA complex

New page

'''Unreleased structure'''

The entry 4ov7 is ON HOLD

Authors: Ortlund, E.A.

Description: Ancestral Steroid Receptor 2 DBD helix mutant -SRE DNA complex