4gat - Revision history

OCA at 09:48, 22 May 2024

OCA — Wed, 22 May 2024 09:48:12 GMT

←Older revision		Revision as of 09:48, 22 May 2024
Line 1:		Line 1:

	==SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE, REGULARIZED MEAN STRUCTURE==		==SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE, REGULARIZED MEAN STRUCTURE==
-	<StructureSection load='4gat' size='340' side='right'caption='[[4gat~~]], [[NMR_Ensembles_of_Models \| 1 NMR models~~]]' scene=''>	+	<StructureSection load='4gat' size='340' side='right'caption='[[4gat]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4gat]] 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=4GAT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GAT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4gat]] 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=4GAT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GAT 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;'~~>~~[[5gat\|5gat]]~~<~~/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=4gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gat OCA], [https://pdbe.org/4gat PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gat RCSB], [https://www.ebi.ac.uk/pdbsum/4gat PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gat 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=4gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gat OCA], [https://pdbe.org/4gat PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gat RCSB], [https://www.ebi.ac.uk/pdbsum/4gat PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gat 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 07:05, 16 March 2022

OCA — Wed, 16 Mar 2022 07:05:06 GMT

←Older revision		Revision as of 07:05, 16 March 2022
Line 1:		Line 1:

	==SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE, REGULARIZED MEAN STRUCTURE==		==SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE, REGULARIZED MEAN STRUCTURE==
-	<StructureSection load='4gat' size='340' side='right' caption='[[4gat]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>	+	<StructureSection load='4gat' size='340' side='right'caption='[[4gat]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4gat]] 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=4GAT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4GAT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4gat]] 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=4GAT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GAT 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">[[5gat\|5gat]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[5gat\|5gat]]</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=4gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gat OCA], [~~http~~://pdbe.org/4gat PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4gat RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4gat PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4gat 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=4gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gat OCA], [https://pdbe.org/4gat PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gat RCSB], [https://www.ebi.ac.uk/pdbsum/4gat PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gat 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/4gat_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ga/4gat_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 35:		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 04:17, 5 August 2016

OCA — Fri, 05 Aug 2016 04:17:11 GMT

←Older revision		Revision as of 04:17, 5 August 2016
Line 1:		Line 1:
		+
	==SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE, REGULARIZED MEAN STRUCTURE==		==SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE, REGULARIZED MEAN STRUCTURE==
	<StructureSection load='4gat' size='340' side='right' caption='[[4gat]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='4gat' size='340' side='right' caption='[[4gat]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4gat]] 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=4GAT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GAT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4gat]] 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=4GAT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GAT 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">[[5gat\|5gat]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gat\|5gat]]</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=4gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gat OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gat RCSB], [http://www.ebi.ac.uk/pdbsum/4gat 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=4gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gat OCA], [http://pdbe.org/4gat PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gat RCSB], [http://www.ebi.ac.uk/pdbsum/4gat PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gat ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<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=4gat ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 29:
	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 4gat" 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 15:45, 25 December 2014

OCA — Thu, 25 Dec 2014 15:45:42 GMT

←Older revision		Revision as of 15:45, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4gat]] 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=4GAT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GAT FirstGlance]. <br>		<table><tr><td colspan='2'>[[4gat]] 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=4GAT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GAT 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">[[5gat\|5gat]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gat\|5gat]]</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=4gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gat OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gat RCSB], [http://www.ebi.ac.uk/pdbsum/4gat 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=4gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gat OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gat RCSB], [http://www.ebi.ac.uk/pdbsum/4gat 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 "4gat" [edit=sysop:move=sysop]

OCA — Thu, 05 Jun 2014 07:34:43 GMT

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

←Older revision

Revision as of 07:34, 5 June 2014

OCA at 07:34, 5 June 2014

OCA — Thu, 05 Jun 2014 07:34:41 GMT

←Older revision		Revision as of 07:34, 5 June 2014
Line 1:		Line 1:
-	~~{{Seed}}~~	+	==SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE, REGULARIZED MEAN STRUCTURE==
-	[[~~Image:~~4gat.~~png~~\|~~left~~\|200px]]	+	<StructureSection load='4gat' size='340' side='right' caption='[[4gat]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4gat]] 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=4GAT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GAT 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">[[5gat\|5gat]]</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=4gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gat OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gat RCSB], [http://www.ebi.ac.uk/pdbsum/4gat 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/4gat_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 solution structure of a complex between the DNA binding domain of a fungal GATA factor and a 13 base-pair oligonucleotide containing its physiologically relevant CGATAG target sequence has been determined by multidimensional nuclear magnetic resonance spectroscopy. The AREA DNA binding domain, from Aspergillus nidulans, possesses a single Cys2-Cys2 zinc finger module and a basic C-terminal tail, which recognize the CGATAG element via an extensive network of hydrophobic interactions with the bases in the major groove and numerous non-specific contacts along the sugar-phosphate backbone. The zinc finger core of the AREA DNA binding domain has the same global fold as that of the C-terminal DNA binding domain of chicken GATA-1. In contrast to the complex with the DNA binding domain of GATA-1 in which the basic C-terminal tail wraps around the DNA and lies in the minor groove, the structure of complex with the AREA DNA binding domain reveals that the C-terminal tail of the fungal domain runs parallel with the sugar phosphate backbone along the edge of the minor groove. This difference is principally attributed to amino acid substitutions at two positions of the AREA DNA binding domain (Val55, Asn62) relative to that of GATA-1 (Gly55, Lys62). The impact of the different C-terminal tail binding modes on the affinity and specificity of GATA factors is discussed.

-	<!--	+	The solution structure of a fungal AREA protein-DNA complex: an alternative binding mode for the basic carboxyl tail of GATA factors.,Starich MR, Wikstrom M, Arst HN Jr, Clore GM, Gronenborn AM J Mol Biol. 1998 Apr 3;277(3):605-20. PMID:9533883<ref>PMID:9533883</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_4gat"~~, ~~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_4gat\| PDB=4gat \| SCENE= }}~~	+

-	~~===SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE~~, ~~REGULARIZED MEAN STRUCTURE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_9533883}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 9533883 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_9533883}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~4GAT 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=4GAT OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:9533883<~~/~~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 20:49:55 2009''

OCA at 18:49, 17 February 2009

OCA — Tue, 17 Feb 2009 18:49:56 GMT

←Older revision		Revision as of 18:49, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	4GAT 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=4GAT OCA].	+	4GAT 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=4GAT OCA].

	==Reference==		==Reference==
-	The solution structure of a fungal AREA protein-DNA complex: an alternative binding mode for the basic carboxyl tail of GATA factors., Starich MR, Wikstrom M, Arst HN Jr, Clore GM, Gronenborn AM, J Mol Biol. 1998 Apr 3;277(3):605-20. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/9533883 9533883]~~	+	<ref group="xtra">PMID:9533883</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 13~~:38:~~04 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 20:49:55 2009''

OCA at 10:38, 3 July 2008

OCA — Thu, 03 Jul 2008 10:38:04 GMT

←Older revision		Revision as of 10:38, 3 July 2008
Line 1:		Line 1:
-	[[Image:4gat.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:4gat.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_4gat\| PDB=4gat \| SCENE= }}		{{STRUCTURE_4gat\| PDB=4gat \| SCENE= }}

-	~~'''~~SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE, REGULARIZED MEAN STRUCTURE~~'''~~	+	===SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE, REGULARIZED MEAN STRUCTURE===


-	~~==Overview==~~	+	<!--
-	The solution structure of a complex between the DNA binding domain of a fungal GATA factor and a 13 base-pair oligonucleotide containing its physiologically relevant CGATAG target sequence has been determined by multidimensional nuclear magnetic resonance spectroscopy. The AREA DNA binding domain, ~~from Aspergillus nidulans, possesses a single Cys2-Cys2 zinc finger module and a basic C-terminal tail~~, ~~which recognize~~ the ~~CGATAG element via an extensive network of hydrophobic interactions with~~ the ~~bases in the major groove and numerous non-specific contacts along the sugar-phosphate backbone. The zinc finger core of the AREA DNA binding domain has the same global fold~~ as ~~that of the C-terminal DNA binding domain of chicken GATA-1~~. ~~In contrast to the complex with the DNA binding domain of GATA-1 in which the basic C-terminal tail wraps around the DNA and lies in the minor groove~~, the structure of complex with the AREA DNA binding domain reveals that the C-terminal tail of the fungal domain runs parallel with the sugar phosphate backbone along the edge of the minor groove. This difference is ~~principally attributed to amino acid substitutions at two positions of~~ the ~~AREA DNA binding domain (Val55, Asn62) relative to that of GATA-1 (Gly55, Lys62)~~. ~~The impact of the different C~~-~~terminal tail binding modes on the affinity and specificity of GATA factors is discussed.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_9533883}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 9533883 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_9533883}}

	==About this Structure==		==About this Structure==
-	4GAT 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=4GAT OCA].	+	4GAT 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=4GAT 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~~:24:21 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 13:38:04 2008''

OCA at 19:24, 4 May 2008

OCA — Sun, 04 May 2008 19:24:22 GMT

←Older revision		Revision as of 19:24, 4 May 2008
Line 1:		Line 1:
	[[Image:4gat.jpg\|left\|200px]]		[[Image:4gat.jpg\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 4gat \|SIZE=350\|CAPTION=~~ <~~scene name='initialview01'>4gat</scene>~~	+	The line below this paragraph, containing "STRUCTURE_4gat", 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_4gat\| PDB=4gat \| SCENE= }}
-	~~\|RELATEDENTRY=[[5gat\|5GAT]]~~	+
-	\|~~RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol~~=4gat ~~FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id~~=~~4gat OCA], [http://www.ebi.ac.uk/pdbsum/4gat PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=4gat RCSB]</span>~~	+
-	}}	+

	'''SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE, REGULARIZED MEAN STRUCTURE'''		'''SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE, REGULARIZED MEAN STRUCTURE'''
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 22:24:21 2008''
-		+
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:38:52 2008''	+

OCA at 02:38, 31 March 2008

OCA — Mon, 31 Mar 2008 02:38:55 GMT

←Older revision		Revision as of 02:38, 31 March 2008
Line 4:		Line 4:
	\|PDB= 4gat \|SIZE=350\|CAPTION= <scene name='initialview01'>4gat</scene>		\|PDB= 4gat \|SIZE=350\|CAPTION= <scene name='initialview01'>4gat</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=[[5gat\|5GAT]]
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4gat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gat OCA], [http://www.ebi.ac.uk/pdbsum/4gat PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=4gat 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~~:09:45 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:38:52 2008''