7gat - Revision history

OCA at 10:36, 22 May 2024

OCA — Wed, 22 May 2024 10:36:15 GMT

←Older revision		Revision as of 10:36, 22 May 2024
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	==SOLUTION NMR STRUCTURE OF THE L22V MUTANT DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13 BP DNA CONTAINING A TGATA SITE, 34 STRUCTURES==		==SOLUTION NMR STRUCTURE OF THE L22V MUTANT DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13 BP DNA CONTAINING A TGATA SITE, 34 STRUCTURES==
-	<StructureSection load='7gat' size='340' side='right'caption='[[7gat~~]], [[NMR_Ensembles_of_Models \| 34 NMR models~~]]' scene=''>	+	<StructureSection load='7gat' size='340' side='right'caption='[[7gat]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7gat]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~A._nidulans A.~~ nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7GAT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7GAT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7gat]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_nidulans Aspergillus nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7GAT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7GAT 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">Solution NMR</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[6gat\|6gat]]~~<~~/div></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">POTENTIAL ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=162425 A. nidulans])~~</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=7gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7gat OCA], [https://pdbe.org/7gat PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7gat RCSB], [https://www.ebi.ac.uk/pdbsum/7gat PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7gat 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=7gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7gat OCA], [https://pdbe.org/7gat PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7gat RCSB], [https://www.ebi.ac.uk/pdbsum/7gat PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7gat ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/AREA_EMENI AREA_EMENI]] Transcription activator that binds the consensus DNA element 5'-CGATAG-3' and mediates nitrogen metabolite repression. Activates the transcription of uapA.<ref>PMID:1970293</ref>	+	[https://www.uniprot.org/uniprot/AREA_EMENI AREA_EMENI] Transcription activator that binds the consensus DNA element 5'-CGATAG-3' and mediates nitrogen metabolite repression. Activates the transcription of uapA.<ref>PMID:1970293</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: A. nidulans]]	+	[[Category: Aspergillus nidulans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Clore~~, G M~~]]	+	[[Category: Clore GM]]
-	[[Category: Gronenborn~~, A M~~]]	+	[[Category: Gronenborn AM]]
-	[[Category: Starich, M]]	+	[[Category: Starich M]]
-	[[Category: Wikstrom, M]]	+	[[Category: Wikstrom M]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Transcription factor]]~~	+
-	~~[[Category: Transcription-dna complex]]~~	+
-	~~[[Category: Zinc binding domain~~]]	+

OCA at 15:58, 3 November 2021

OCA — Wed, 03 Nov 2021 15:58:23 GMT

←Older revision		Revision as of 15:58, 3 November 2021
Line 1:		Line 1:
		+
	==SOLUTION NMR STRUCTURE OF THE L22V MUTANT DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13 BP DNA CONTAINING A TGATA SITE, 34 STRUCTURES==		==SOLUTION NMR STRUCTURE OF THE L22V MUTANT DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13 BP DNA CONTAINING A TGATA SITE, 34 STRUCTURES==
-	<StructureSection load='7gat' size='340' side='right' caption='[[7gat]], [[NMR_Ensembles_of_Models \| 34 NMR models]]' scene=''>	+	<StructureSection load='7gat' size='340' side='right'caption='[[7gat]], [[NMR_Ensembles_of_Models \| 34 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7gat]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/A._nidulans A. nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7GAT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=7GAT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7gat]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/A._nidulans A. nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7GAT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7GAT 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">[[6gat\|6gat]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6gat\|6gat]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POTENTIAL ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=162425 A. nidulans])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POTENTIAL ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=162425 A. nidulans])</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=7gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7gat OCA], [~~http~~://pdbe.org/7gat PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7gat RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7gat PDBsum]</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=7gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7gat OCA], [https://pdbe.org/7gat PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7gat RCSB], [https://www.ebi.ac.uk/pdbsum/7gat PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7gat ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/AREA_EMENI AREA_EMENI]] Transcription activator that binds the consensus DNA element 5'-CGATAG-3' and mediates nitrogen metabolite repression. Activates the transcription of uapA.<ref>PMID:1970293</ref>	+	[[https://www.uniprot.org/uniprot/AREA_EMENI AREA_EMENI]] Transcription activator that binds the consensus DNA element 5'-CGATAG-3' and mediates nitrogen metabolite repression. Activates the transcription of uapA.<ref>PMID:1970293</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ga/7gat_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ga/7gat_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 34:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: A. nidulans]]		[[Category: A. nidulans]]
		+	[[Category: Large Structures]]
	[[Category: Clore, G M]]		[[Category: Clore, G M]]
	[[Category: Gronenborn, A M]]		[[Category: Gronenborn, A M]]

OCA at 05:32, 9 February 2016

OCA — Tue, 09 Feb 2016 05:32:03 GMT

←Older revision		Revision as of 05:32, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='7gat' size='340' side='right' caption='[[7gat]], [[NMR_Ensembles_of_Models \| 34 NMR models]]' scene=''>		<StructureSection load='7gat' size='340' side='right' caption='[[7gat]], [[NMR_Ensembles_of_Models \| 34 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7gat]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Emericella_nidulans Emericella~~ nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7GAT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7GAT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7gat]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/A._nidulans A. nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7GAT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7GAT 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">[[6gat\|6gat]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6gat\|6gat]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POTENTIAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=162425 ~~Emericella~~ nidulans])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POTENTIAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=162425 A. nidulans])</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=7gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7gat OCA], [http://www.rcsb.org/pdb/explore.do?structureId=7gat RCSB], [http://www.ebi.ac.uk/pdbsum/7gat 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=7gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7gat OCA], [http://pdbe.org/7gat PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7gat RCSB], [http://www.ebi.ac.uk/pdbsum/7gat PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=7gat ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	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 7gat" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Emericella~~ nidulans]]	+	[[Category: A. nidulans]]
	[[Category: Clore, G M]]		[[Category: Clore, G M]]
	[[Category: Gronenborn, A M]]		[[Category: Gronenborn, A M]]

OCA at 04:46, 25 December 2014

OCA — Thu, 25 Dec 2014 04:46:00 GMT

←Older revision		Revision as of 04:46, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7gat]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Emericella_nidulans Emericella nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7GAT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7GAT FirstGlance]. <br>		<table><tr><td colspan='2'>[[7gat]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Emericella_nidulans Emericella nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7GAT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7GAT FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><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><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6gat\|6gat]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6gat\|6gat]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POTENTIAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=162425 Emericella nidulans])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POTENTIAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=162425 Emericella nidulans])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7gat OCA], [http://www.rcsb.org/pdb/explore.do?structureId=7gat RCSB], [http://www.ebi.ac.uk/pdbsum/7gat 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=7gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7gat OCA], [http://www.rcsb.org/pdb/explore.do?structureId=7gat RCSB], [http://www.ebi.ac.uk/pdbsum/7gat PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AREA_EMENI AREA_EMENI]] Transcription activator that binds the consensus DNA element 5'-CGATAG-3' and mediates nitrogen metabolite repression. Activates the transcription of uapA.<ref>PMID:1970293</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Emericella nidulans]]		[[Category: Emericella nidulans]]
-	[[Category: Clore, G M.]]	+	[[Category: Clore, G M]]
-	[[Category: Gronenborn, A M.]]	+	[[Category: Gronenborn, A M]]
-	[[Category: Starich, M.]]	+	[[Category: Starich, M]]
-	[[Category: Wikstrom, M.]]	+	[[Category: Wikstrom, M]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: Transcription factor]]		[[Category: Transcription factor]]
	[[Category: Transcription-dna complex]]		[[Category: Transcription-dna complex]]
	[[Category: Zinc binding domain]]		[[Category: Zinc binding domain]]

OCA: Protected "7gat" [edit=sysop:move=sysop]

OCA — Thu, 05 Jun 2014 07:30:01 GMT

Protected "7gat" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:30, 5 June 2014

OCA at 07:29, 5 June 2014

OCA — Thu, 05 Jun 2014 07:29:59 GMT

←Older revision		Revision as of 07:29, 5 June 2014
Line 1:		Line 1:
-	~~{{Seed}}~~	+	==SOLUTION NMR STRUCTURE OF THE L22V MUTANT DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13 BP DNA CONTAINING A TGATA SITE, 34 STRUCTURES==
-	[[~~Image:~~7gat.~~png~~\|~~left~~\|200px]]	+	<StructureSection load='7gat' size='340' side='right' caption='[[7gat]], [[NMR_Ensembles_of_Models \| 34 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7gat]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Emericella_nidulans Emericella nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7GAT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7GAT FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6gat\|6gat]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POTENTIAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=162425 Emericella nidulans])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7gat OCA], [http://www.rcsb.org/pdb/explore.do?structureId=7gat RCSB], [http://www.ebi.ac.uk/pdbsum/7gat PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ga/7gat_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The seemingly innocuous leucine-to-valine mutation at position 22 of the AREA DNA binding domain results in dramatic changes in the in vivo expression profile of genes controlled by this GATA transcription factor. This is associated with a preference of the Leu22-->Val mutant for TGATAG sites over (A/C)GATAG sites. Quantitative gel retardation assays confirm this observation and show that the Leu22-->Val mutant AREA DNA binding domain has a approximately 30-fold lower affinity than the wild-type domain for a 13 base-pair oligonucleotide containing the wild-type CGATAG target. To gain insight into the measured affinity data and further explore sequence specificity of the AREA protein, the solution structure of a complex between the Leu22-->Val mutant AREA DNA binding domain and a 13 base-pair oligonucleotide containing its physiologically relevant TGATAG target sequence has been determined by multidimensional nuclear magnetic resonance spectroscopy. Comparison of this structure with that of the wild-type AREA DNA binding domain complexed to its cognate CGATAG target site shows how subtle changes in amino acid side-chain length and hydrophobic packing can affect affinity and specificity for GATA-containing sequences, and how changes in DNA sequence can be compensated for by changes in protein sequence.

-	<!--	+	The solution structure of the Leu22-->Val mutant AREA DNA binding domain complexed with a TGATAG core element defines a role for hydrophobic packing in the determination of specificity.,Starich MR, Wikstrom M, Schumacher S, Arst HN Jr, Gronenborn AM, Clore GM J Mol Biol. 1998 Apr 3;277(3):621-34. PMID:9533884<ref>PMID:9533884</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_7gat"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display~~.	+
-	-->	+
-	~~{{STRUCTURE_7gat\| PDB=7gat \| SCENE= }}~~	+

-	~~===SOLUTION NMR STRUCTURE OF THE L22V MUTANT DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13 BP DNA CONTAINING A TGATA SITE~~, ~~34 STRUCTURES===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_9533884}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 9533884 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_9533884}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~7GAT is a 3 chains structure of sequences from [http:~~/~~/en.wikipedia.org/wiki/Emericella_nidulans Emericella nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7GAT OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:9533884<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Emericella nidulans]]		[[Category: Emericella nidulans]]
	[[Category: Clore, G M.]]		[[Category: Clore, G M.]]
Line 31:		Line 37:
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: Transcription factor]]		[[Category: Transcription factor]]
		+	[[Category: Transcription-dna complex]]
	[[Category: Zinc binding domain]]		[[Category: Zinc binding domain]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:51:56 2009''

OCA at 04:51, 17 February 2009

OCA — Tue, 17 Feb 2009 04:51:58 GMT

←Older revision		Revision as of 04:51, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	7GAT is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Emericella_nidulans Emericella nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7GAT OCA].	+	7GAT is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Emericella_nidulans Emericella nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7GAT OCA].

	==Reference==		==Reference==
-	The solution structure of the Leu22-->Val mutant AREA DNA binding domain complexed with a TGATAG core element defines a role for hydrophobic packing in the determination of specificity., Starich MR, Wikstrom M, Schumacher S, Arst HN Jr, Gronenborn AM, Clore GM, J Mol Biol. 1998 Apr 3;277(3):621-34. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/9533884 9533884]~~	+	<ref group="xtra">PMID:9533884</ref><references group="xtra"/>
	[[Category: Emericella nidulans]]		[[Category: Emericella nidulans]]
-	[[Category: Single protein]]
	[[Category: Clore, G M.]]		[[Category: Clore, G M.]]
	[[Category: Gronenborn, A M.]]		[[Category: Gronenborn, A M.]]
Line 34:		Line 33:
	[[Category: Zinc binding domain]]		[[Category: Zinc binding domain]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 3 14~~:33:~~10 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:51:56 2009''

OCA at 11:33, 3 July 2008

OCA — Thu, 03 Jul 2008 11:33:10 GMT

←Older revision		Revision as of 11:33, 3 July 2008
Line 1:		Line 1:
-	[[Image:7gat.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:7gat.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_7gat\| PDB=7gat \| SCENE= }}		{{STRUCTURE_7gat\| PDB=7gat \| SCENE= }}

-	~~'''~~SOLUTION NMR STRUCTURE OF THE L22V MUTANT DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13 BP DNA CONTAINING A TGATA SITE, 34 STRUCTURES~~'''~~	+	===SOLUTION NMR STRUCTURE OF THE L22V MUTANT DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13 BP DNA CONTAINING A TGATA SITE, 34 STRUCTURES===


-	~~==Overview==~~	+	<!--
-	The ~~seemingly innocuous leucine-~~to~~-valine mutation at position 22 of~~ the AREA DNA binding domain results in dramatic changes in the in vivo expression profile of genes controlled by this GATA transcription factor. This is associated with a preference of the Leu22-->Val mutant for TGATAG sites over (A/~~C)GATAG sites~~. Quantitative gel retardation assays confirm this observation and show that the Leu22-->Val mutant AREA DNA binding domain has a approximately 30-fold lower affinity than the wild-type domain for a 13 base-pair oligonucleotide containing the wild-type CGATAG target. ~~To gain insight into the measured affinity data and further explore sequence specificity of the AREA protein~~, the solution structure of a complex between the Leu22-->Val mutant AREA DNA binding domain and a 13 base-pair oligonucleotide containing its physiologically relevant TGATAG target sequence has been determined by multidimensional nuclear magnetic resonance spectroscopy. ~~Comparison of this structure with that of the wild~~-~~type AREA DNA binding domain complexed to its cognate CGATAG target site shows how subtle changes in amino acid side~~-~~chain length and hydrophobic packing can affect affinity and specificity for GATA-containing sequences, and how changes in DNA sequence can be compensated for by changes in protein sequence.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_9533884}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 9533884 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_9533884}}

	==About this Structure==		==About this Structure==
-	7GAT is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Emericella_nidulans Emericella nidulans]. Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7GAT OCA].	+	7GAT is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Emericella_nidulans Emericella nidulans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7GAT OCA].

	==Reference==		==Reference==
Line 29:		Line 33:
	[[Category: Transcription factor]]		[[Category: Transcription factor]]
	[[Category: Zinc binding domain]]		[[Category: Zinc binding domain]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:44:50 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 14:33:10 2008''

OCA at 19:44, 4 May 2008

OCA — Sun, 04 May 2008 19:44:51 GMT

←Older revision		Revision as of 19:44, 4 May 2008
Line 1:		Line 1:
	[[Image:7gat.gif\|left\|200px]]		[[Image:7gat.gif\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 7gat \|SIZE=350\|CAPTION=~~ <~~scene name='initialview01'>7gat</scene>~~	+	The line below this paragraph, containing "STRUCTURE_7gat", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <scene name='pdbligand=DA:2'~~-~~DEOXYADENOSINE~~-~~5'-MONOPHOSPHATE'>DA</scene>~~, ~~<scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>~~, ~~<scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	~~\|ACTIVITY=~~	+	or leave the SCENE parameter empty for the default display.
-	~~\|GENE= POTENTIAL~~ (~~[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=162425 Emericella nidulans]~~)	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_7gat\| PDB=7gat \| SCENE= }}
-	~~\|RELATEDENTRY=[[6gat\|6GAT]]~~	+
-	\|~~RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol~~=7gat ~~FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id~~=~~7gat OCA], [http://www.ebi.ac.uk/pdbsum/7gat PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=7gat RCSB]</span>~~	+
-	}}	+

	'''SOLUTION NMR STRUCTURE OF THE L22V MUTANT DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13 BP DNA CONTAINING A TGATA SITE, 34 STRUCTURES'''		'''SOLUTION NMR STRUCTURE OF THE L22V MUTANT DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13 BP DNA CONTAINING A TGATA SITE, 34 STRUCTURES'''
Line 29:		Line 26:
	[[Category: Starich, M.]]		[[Category: Starich, M.]]
	[[Category: Wikstrom, M.]]		[[Category: Wikstrom, M.]]
-	[[Category: ~~complex (transcription regulation/dna)]]~~	+	[[Category: Dna binding protein]]
-	~~[[Category: dna~~ binding protein]]	+	[[Category: Transcription factor]]
-	[[Category: ~~transcription~~ factor]]	+	[[Category: Zinc binding domain]]
-	[[Category: ~~zinc~~ binding domain]]	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:44:50 2008''
-		+
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:44:03 2008''	+

OCA at 02:44, 31 March 2008

OCA — Mon, 31 Mar 2008 02:44:06 GMT

←Older revision		Revision as of 02:44, 31 March 2008
Line 4:		Line 4:
	\|PDB= 7gat \|SIZE=350\|CAPTION= <scene name='initialview01'>7gat</scene>		\|PDB= 7gat \|SIZE=350\|CAPTION= <scene name='initialview01'>7gat</scene>
	\|SITE=		\|SITE=
-	\|LIGAND= <scene name='pdbligand=ZN:ZINC ION'>ZN</scene>	+	\|LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE= POTENTIAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=162425 Emericella nidulans])		\|GENE= POTENTIAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=162425 Emericella nidulans])
		+	\|DOMAIN=
		+	\|RELATEDENTRY=[[6gat\|6GAT]]
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7gat OCA], [http://www.ebi.ac.uk/pdbsum/7gat PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=7gat RCSB]</span>
	}}		}}

Line 26:		Line 29:
	[[Category: Starich, M.]]		[[Category: Starich, M.]]
	[[Category: Wikstrom, M.]]		[[Category: Wikstrom, M.]]
-	[[Category: ZN]]
	[[Category: complex (transcription regulation/dna)]]		[[Category: complex (transcription regulation/dna)]]
	[[Category: dna binding protein]]		[[Category: dna binding protein]]
Line 32:		Line 34:
	[[Category: zinc binding domain]]		[[Category: zinc binding domain]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Mar ~~20 19~~:14:34 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:44:03 2008''