1srk - Revision history

OCA at 09:09, 22 May 2024

OCA — Wed, 22 May 2024 09:09:34 GMT

←Older revision		Revision as of 09:09, 22 May 2024
Line 20:		Line 20:
	</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=1srk 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=1srk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Classic zinc finger domains (cZFs) consist of a beta-hairpin followed by an alpha-helix. They are among the most abundant of all protein domains and are often found in tandem arrays in DNA-binding proteins, with each finger contributing an alpha-helix to effect sequence-specific DNA recognition. Lone cZFs, not found in tandem arrays, have been postulated to function in protein interactions. We have studied the transcriptional co-regulator Friend of GATA (FOG), which contains nine zinc fingers. We have discovered that the third cZF of FOG contacts a coiled-coil domain in the centrosomal protein transforming acidic coiled-coil 3 (TACC3). Although FOG-ZF3 exhibited low solubility, we have used a combination of mutational mapping and protein engineering to generate a derivative that was suitable for in vitro and structural analysis. We report that the alpha-helix of FOG-ZF3 recognizes a C-terminal portion of the TACC3 coiled-coil. Remarkably, the alpha-helical surface utilized by FOG-ZF3 is the same surface responsible for the well established sequence-specific DNA-binding properties of many other cZFs. Our data demonstrate the versatility of cZFs and have implications for the analysis of many as yet uncharacterized cZF proteins.
		+
		+	A classic zinc finger from friend of GATA mediates an interaction with the coiled-coil of transforming acidic coiled-coil 3.,Simpson RJ, Yi Lee SH, Bartle N, Sum EY, Visvader JE, Matthews JM, Mackay JP, Crossley M J Biol Chem. 2004 Sep 17;279(38):39789-97. Epub 2004 Jul 2. PMID:15234987<ref>PMID:15234987</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1srk" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:34, 1 May 2024

OCA — Wed, 01 May 2024 08:34:41 GMT

←Older revision		Revision as of 08:34, 1 May 2024
Line 1:		Line 1:

	==Solution structure of the third zinc finger domain of FOG-1==		==Solution structure of the third zinc finger domain of FOG-1==
-	<StructureSection load='1srk' size='340' side='right'caption='[[1srk~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='1srk' size='340' side='right'caption='[[1srk]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1srk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SRK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1srk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SRK 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='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~ZFPM1, FOG1, FOG ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])~~</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=1srk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srk OCA], [https://pdbe.org/1srk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1srk RCSB], [https://www.ebi.ac.uk/pdbsum/1srk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1srk 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=1srk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srk OCA], [https://pdbe.org/1srk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1srk RCSB], [https://www.ebi.ac.uk/pdbsum/1srk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1srk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/FOG1_MOUSE FOG1_MOUSE]] Transcription regulator that plays an essential role in erythroid and megakaryocytic cell differentiation. Essential cofactor that acts via the formation of a heterodimer with transcription factors of the GATA family GATA1, GATA2 and GATA3. Such heterodimer can both activate or repress transcriptional activity, depending on the cell and promoter context. The heterodimer formed with GATA proteins is essential to activate expression of genes such as NFE2, ITGA2B, alpha- and beta-globin, while it represses expression of KLF1. May be involved in regulation of some genes in gonads. May also be involved in cardiac development, in a non-redundant way with ZFPM2/FOG2.<ref>PMID:9230307</ref> <ref>PMID:9553047</ref> <ref>PMID:10078204</ref> <ref>PMID:10329627</ref> <ref>PMID:11940669</ref> <ref>PMID:12356738</ref> <ref>PMID:14614148</ref>	+	[https://www.uniprot.org/uniprot/FOG1_MOUSE FOG1_MOUSE] Transcription regulator that plays an essential role in erythroid and megakaryocytic cell differentiation. Essential cofactor that acts via the formation of a heterodimer with transcription factors of the GATA family GATA1, GATA2 and GATA3. Such heterodimer can both activate or repress transcriptional activity, depending on the cell and promoter context. The heterodimer formed with GATA proteins is essential to activate expression of genes such as NFE2, ITGA2B, alpha- and beta-globin, while it represses expression of KLF1. May be involved in regulation of some genes in gonads. May also be involved in cardiac development, in a non-redundant way with ZFPM2/FOG2.<ref>PMID:9230307</ref> <ref>PMID:9553047</ref> <ref>PMID:10078204</ref> <ref>PMID:10329627</ref> <ref>PMID:11940669</ref> <ref>PMID:12356738</ref> <ref>PMID:14614148</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</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=1srk 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=1srk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Classic zinc finger domains (cZFs) consist of a beta-hairpin followed by an alpha-helix. They are among the most abundant of all protein domains and are often found in tandem arrays in DNA-binding proteins, with each finger contributing an alpha-helix to effect sequence-specific DNA recognition. Lone cZFs, not found in tandem arrays, have been postulated to function in protein interactions. We have studied the transcriptional co-regulator Friend of GATA (FOG), which contains nine zinc fingers. We have discovered that the third cZF of FOG contacts a coiled-coil domain in the centrosomal protein transforming acidic coiled-coil 3 (TACC3). Although FOG-ZF3 exhibited low solubility, we have used a combination of mutational mapping and protein engineering to generate a derivative that was suitable for in vitro and structural analysis. We report that the alpha-helix of FOG-ZF3 recognizes a C-terminal portion of the TACC3 coiled-coil. Remarkably, the alpha-helical surface utilized by FOG-ZF3 is the same surface responsible for the well established sequence-specific DNA-binding properties of many other cZFs. Our data demonstrate the versatility of cZFs and have implications for the analysis of many as yet uncharacterized cZF proteins.
-
-	A classic zinc finger from friend of GATA mediates an interaction with the coiled-coil of transforming acidic coiled-coil 3.,Simpson RJ, Yi Lee SH, Bartle N, Sum EY, Visvader JE, Matthews JM, Mackay JP, Crossley M J Biol Chem. 2004 Sep 17;279(38):39789-97. Epub 2004 Jul 2. PMID:15234987<ref>PMID:15234987</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1srk" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Bartle, N]]	+	[[Category: Bartle N]]
-	[[Category: Crossley, M]]	+	[[Category: Crossley M]]
-	[[Category: Lee~~, S H.Y~~]]	+	[[Category: Lee SHY]]
-	[[Category: Mackay~~, J P~~]]	+	[[Category: Mackay JP]]
-	[[Category: Matthews~~, J M~~]]	+	[[Category: Matthews JM]]
-	[[Category: Simpson~~, R J.Y]]~~	+	[[Category: Simpson RJY]]
-	~~[[Category: Classical zinc finger]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 15:34, 27 October 2021

OCA — Wed, 27 Oct 2021 15:34:22 GMT

←Older revision		Revision as of 15:34, 27 October 2021
Line 3:		Line 3:
	<StructureSection load='1srk' size='340' side='right'caption='[[1srk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1srk' size='340' side='right'caption='[[1srk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1srk]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1SRK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1srk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SRK 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='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">ZFPM1, FOG1, FOG ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ZFPM1, FOG1, FOG ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1srk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srk OCA], [~~http~~://pdbe.org/1srk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1srk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1srk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1srk 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=1srk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srk OCA], [https://pdbe.org/1srk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1srk RCSB], [https://www.ebi.ac.uk/pdbsum/1srk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1srk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/FOG1_MOUSE FOG1_MOUSE]] Transcription regulator that plays an essential role in erythroid and megakaryocytic cell differentiation. Essential cofactor that acts via the formation of a heterodimer with transcription factors of the GATA family GATA1, GATA2 and GATA3. Such heterodimer can both activate or repress transcriptional activity, depending on the cell and promoter context. The heterodimer formed with GATA proteins is essential to activate expression of genes such as NFE2, ITGA2B, alpha- and beta-globin, while it represses expression of KLF1. May be involved in regulation of some genes in gonads. May also be involved in cardiac development, in a non-redundant way with ZFPM2/FOG2.<ref>PMID:9230307</ref> <ref>PMID:9553047</ref> <ref>PMID:10078204</ref> <ref>PMID:10329627</ref> <ref>PMID:11940669</ref> <ref>PMID:12356738</ref> <ref>PMID:14614148</ref>	+	[[https://www.uniprot.org/uniprot/FOG1_MOUSE FOG1_MOUSE]] Transcription regulator that plays an essential role in erythroid and megakaryocytic cell differentiation. Essential cofactor that acts via the formation of a heterodimer with transcription factors of the GATA family GATA1, GATA2 and GATA3. Such heterodimer can both activate or repress transcriptional activity, depending on the cell and promoter context. The heterodimer formed with GATA proteins is essential to activate expression of genes such as NFE2, ITGA2B, alpha- and beta-globin, while it represses expression of KLF1. May be involved in regulation of some genes in gonads. May also be involved in cardiac development, in a non-redundant way with ZFPM2/FOG2.<ref>PMID:9230307</ref> <ref>PMID:9553047</ref> <ref>PMID:10078204</ref> <ref>PMID:10329627</ref> <ref>PMID:11940669</ref> <ref>PMID:12356738</ref> <ref>PMID:14614148</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 11:32, 24 December 2020

OCA — Thu, 24 Dec 2020 11:32:49 GMT

←Older revision		Revision as of 11:32, 24 December 2020
Line 1:		Line 1:

	==Solution structure of the third zinc finger domain of FOG-1==		==Solution structure of the third zinc finger domain of FOG-1==
-	<StructureSection load='1srk' size='340' side='right' caption='[[1srk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='1srk' size='340' side='right'caption='[[1srk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1srk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1SRK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1srk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1SRK 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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ZFPM1, FOG1, FOG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ZFPM1, FOG1, FOG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=1srk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srk OCA], [http://pdbe.org/1srk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1srk RCSB], [http://www.ebi.ac.uk/pdbsum/1srk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1srk ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1srk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srk OCA], [http://pdbe.org/1srk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1srk RCSB], [http://www.ebi.ac.uk/pdbsum/1srk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1srk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lk3 transgenic mice]]		[[Category: Lk3 transgenic mice]]
	[[Category: Bartle, N]]		[[Category: Bartle, N]]

OCA at 07:34, 14 March 2018

OCA — Wed, 14 Mar 2018 07:34:46 GMT

←Older revision		Revision as of 07:34, 14 March 2018
Line 1:		Line 1:
		+
	==Solution structure of the third zinc finger domain of FOG-1==		==Solution structure of the third zinc finger domain of FOG-1==
	<StructureSection load='1srk' size='340' side='right' caption='[[1srk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1srk' size='340' side='right' caption='[[1srk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' 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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ZFPM1, FOG1, FOG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ZFPM1, FOG1, FOG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=1srk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srk OCA], [http://pdbe.org/1srk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1srk RCSB], [http://www.ebi.ac.uk/pdbsum/1srk 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=1srk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srk OCA], [http://pdbe.org/1srk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1srk RCSB], [http://www.ebi.ac.uk/pdbsum/1srk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1srk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sr/1srk_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sr/1srk_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>
	</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=1srk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:49, 11 September 2015

OCA — Fri, 11 Sep 2015 09:49:08 GMT

←Older revision		Revision as of 09:49, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1srk' size='340' side='right' caption='[[1srk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1srk' size='340' side='right' caption='[[1srk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1srk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mus_musculus Mus musculus~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SRK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1srk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SRK 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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ZFPM1, FOG1, FOG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 ~~Mus musculus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ZFPM1, FOG1, FOG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=1srk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1srk RCSB], [http://www.ebi.ac.uk/pdbsum/1srk 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=1srk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srk OCA], [http://pdbe.org/1srk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1srk RCSB], [http://www.ebi.ac.uk/pdbsum/1srk PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 1srk" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Mus musculus~~]]	+	[[Category: Lk3 transgenic mice]]
	[[Category: Bartle, N]]		[[Category: Bartle, N]]
	[[Category: Crossley, M]]		[[Category: Crossley, M]]

OCA at 14:44, 25 December 2014

OCA — Thu, 25 Dec 2014 14:44:03 GMT

←Older revision		Revision as of 14:44, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1srk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SRK FirstGlance]. <br>		<table><tr><td colspan='2'>[[1srk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SRK 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>[[Gene\|Gene:]]</b></td><td class="sblockDat">ZFPM1, FOG1, FOG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ZFPM1, FOG1, FOG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])</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=1srk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1srk RCSB], [http://www.ebi.ac.uk/pdbsum/1srk 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=1srk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1srk RCSB], [http://www.ebi.ac.uk/pdbsum/1srk PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FOG1_MOUSE FOG1_MOUSE]] Transcription regulator that plays an essential role in erythroid and megakaryocytic cell differentiation. Essential cofactor that acts via the formation of a heterodimer with transcription factors of the GATA family GATA1, GATA2 and GATA3. Such heterodimer can both activate or repress transcriptional activity, depending on the cell and promoter context. The heterodimer formed with GATA proteins is essential to activate expression of genes such as NFE2, ITGA2B, alpha- and beta-globin, while it represses expression of KLF1. May be involved in regulation of some genes in gonads. May also be involved in cardiac development, in a non-redundant way with ZFPM2/FOG2.<ref>PMID:9230307</ref> <ref>PMID:9553047</ref> <ref>PMID:10078204</ref> <ref>PMID:10329627</ref> <ref>PMID:11940669</ref> <ref>PMID:12356738</ref> <ref>PMID:14614148</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Bartle, N.]]	+	[[Category: Bartle, N]]
-	[[Category: Crossley, M.]]	+	[[Category: Crossley, M]]
-	[[Category: Lee, S H.Y.]]	+	[[Category: Lee, S H.Y]]
-	[[Category: Mackay, J P.]]	+	[[Category: Mackay, J P]]
-	[[Category: Matthews, J M.]]	+	[[Category: Matthews, J M]]
-	[[Category: Simpson, R J.Y.]]	+	[[Category: Simpson, R J.Y]]
	[[Category: Classical zinc finger]]		[[Category: Classical zinc finger]]
	[[Category: Transcription]]		[[Category: Transcription]]

OCA at 17:20, 29 September 2014

OCA — Mon, 29 Sep 2014 17:20:56 GMT

←Older revision		Revision as of 17:20, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1srk.~~png~~\|~~left~~\|200px]]	+	==Solution structure of the third zinc finger domain of FOG-1==
		+	<StructureSection load='1srk' size='340' side='right' caption='[[1srk]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1srk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SRK 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>[[Gene\|Gene:]]</b></td><td class="sblockDat">ZFPM1, FOG1, FOG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])</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=1srk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1srk RCSB], [http://www.ebi.ac.uk/pdbsum/1srk 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/sr/1srk_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 ==
		+	Classic zinc finger domains (cZFs) consist of a beta-hairpin followed by an alpha-helix. They are among the most abundant of all protein domains and are often found in tandem arrays in DNA-binding proteins, with each finger contributing an alpha-helix to effect sequence-specific DNA recognition. Lone cZFs, not found in tandem arrays, have been postulated to function in protein interactions. We have studied the transcriptional co-regulator Friend of GATA (FOG), which contains nine zinc fingers. We have discovered that the third cZF of FOG contacts a coiled-coil domain in the centrosomal protein transforming acidic coiled-coil 3 (TACC3). Although FOG-ZF3 exhibited low solubility, we have used a combination of mutational mapping and protein engineering to generate a derivative that was suitable for in vitro and structural analysis. We report that the alpha-helix of FOG-ZF3 recognizes a C-terminal portion of the TACC3 coiled-coil. Remarkably, the alpha-helical surface utilized by FOG-ZF3 is the same surface responsible for the well established sequence-specific DNA-binding properties of many other cZFs. Our data demonstrate the versatility of cZFs and have implications for the analysis of many as yet uncharacterized cZF proteins.

-	~~{{STRUCTURE_1srk\| PDB=1srk \| SCENE= }}~~	+	A classic zinc finger from friend of GATA mediates an interaction with the coiled-coil of transforming acidic coiled-coil 3.,Simpson RJ, Yi Lee SH, Bartle N, Sum EY, Visvader JE, Matthews JM, Mackay JP, Crossley M J Biol Chem. 2004 Sep 17;279(38):39789-97. Epub 2004 Jul 2. PMID:15234987<ref>PMID:15234987</ref>

-	~~===Solution structure~~ of the ~~third zinc finger domain of FOG-1===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15234987}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1srk]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mus_musculus Mus musculus]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1SRK OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015234987<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Bartle, N.]]		[[Category: Bartle, N.]]

OCA: Protected "1srk" [edit=sysop:move=sysop]

OCA — Fri, 04 Jan 2013 10:10:53 GMT

Protected "1srk" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:10, 4 January 2013

OCA at 10:10, 4 January 2013

OCA — Fri, 04 Jan 2013 10:10:50 GMT

←Older revision		Revision as of 10:10, 4 January 2013
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-	{{Seed}}
	[[Image:1srk.png\|left\|200px]]		[[Image:1srk.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1srk", 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_1srk\| PDB=1srk \| SCENE= }}		{{STRUCTURE_1srk\| PDB=1srk \| SCENE= }}

	===Solution structure of the third zinc finger domain of FOG-1===		===Solution structure of the third zinc finger domain of FOG-1===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15234987}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15234987 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15234987}}		{{ABSTRACT_PUBMED_15234987}}

	==About this Structure==		==About this Structure==
-	~~1SRK~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRK OCA].	+	[[1srk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRK OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15234987~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015234987</ref><references group="xtra"/>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Bartle, N.]]		[[Category: Bartle, N.]]
Line 32:		Line 20:
	[[Category: Simpson, R J.Y.]]		[[Category: Simpson, R J.Y.]]
	[[Category: Classical zinc finger]]		[[Category: Classical zinc finger]]
-		+	[[Category: Transcription]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 19:01:26 2009''~~	+