1ysf - Revision history

OCA at 08:05, 15 May 2024

2024-05-15T08:05:39Z

←Older revision		Revision as of 08:05, 15 May 2024
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	==The solution structure of the N-domain of the transcription factor abrB==		==The solution structure of the N-domain of the transcription factor abrB==
-	<StructureSection load='1ysf' size='340' side='right'caption='[[1ysf~~]], [[NMR_Ensembles_of_Models \| 22 NMR models~~]]' scene=''>	+	<StructureSection load='1ysf' size='340' side='right'caption='[[1ysf]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ysf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"vibrio_subtilis"_ehrenberg_1835 "vibrio~~ subtilis~~" ehrenberg 1835~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YSF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YSF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ysf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YSF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YSF FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1ekt\|1ekt]], [[1yfb\|1yfb]]</div></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">ABRB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])~~</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=1ysf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ysf OCA], [https://pdbe.org/1ysf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ysf RCSB], [https://www.ebi.ac.uk/pdbsum/1ysf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ysf 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=1ysf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ysf OCA], [https://pdbe.org/1ysf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ysf RCSB], [https://www.ebi.ac.uk/pdbsum/1ysf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ysf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ABRB_BACSU ABRB_BACSU]] Ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation. It controls the expression of genes spovG and tycA. AbrB binds to the tycA promoter region at two A- and T-rich sites, it may be the sole repressor of tycA transcription.<ref>PMID:2504584</ref>	+	[https://www.uniprot.org/uniprot/ABRB_BACSU ABRB_BACSU] Ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation. It controls the expression of genes spovG and tycA. AbrB binds to the tycA promoter region at two A- and T-rich sites, it may be the sole repressor of tycA transcription.<ref>PMID:2504584</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Vibrio~~ subtilis ~~ehrenberg 1835~~]]	+	[[Category: Bacillus subtilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Coles, M]]	+	[[Category: Coles M]]
-	[[Category: Djuranovic, S]]	+	[[Category: Djuranovic S]]
-	[[Category: Truffault, V]]	+	[[Category: Truffault V]]
-	~~[[Category: Bioinformatic]]~~	+
-	~~[[Category: Homodimer]]~~	+
-	~~[[Category: Nmr]]~~	+
-	~~[[Category: Swapped-hairpin barrel]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 07:13, 2 March 2022

2022-03-02T07:13:17Z

←Older revision		Revision as of 07:13, 2 March 2022
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	<StructureSection load='1ysf' size='340' side='right'caption='[[1ysf]], [[NMR_Ensembles_of_Models \| 22 NMR models]]' scene=''>		<StructureSection load='1ysf' size='340' side='right'caption='[[1ysf]], [[NMR_Ensembles_of_Models \| 22 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ysf]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YSF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1YSF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ysf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YSF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YSF FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ekt\|1ekt]], [[1yfb\|1yfb]]</div></td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ekt\|1ekt]], [[1yfb\|1yfb]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABRB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABRB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=1ysf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ysf OCA], [~~http~~://pdbe.org/1ysf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ysf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ysf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ysf 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=1ysf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ysf OCA], [https://pdbe.org/1ysf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ysf RCSB], [https://www.ebi.ac.uk/pdbsum/1ysf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ysf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ABRB_BACSU ABRB_BACSU]] Ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation. It controls the expression of genes spovG and tycA. AbrB binds to the tycA promoter region at two A- and T-rich sites, it may be the sole repressor of tycA transcription.<ref>PMID:2504584</ref>	+	[[https://www.uniprot.org/uniprot/ABRB_BACSU ABRB_BACSU]] Ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation. It controls the expression of genes spovG and tycA. AbrB binds to the tycA promoter region at two A- and T-rich sites, it may be the sole repressor of tycA transcription.<ref>PMID:2504584</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:51, 20 January 2021

2021-01-20T08:51:32Z

←Older revision		Revision as of 08:51, 20 January 2021
Line 1:		Line 1:

	==The solution structure of the N-domain of the transcription factor abrB==		==The solution structure of the N-domain of the transcription factor abrB==
-	<StructureSection load='1ysf' size='340' side='right' caption='[[1ysf]], [[NMR_Ensembles_of_Models \| 22 NMR models]]' scene=''>	+	<StructureSection load='1ysf' size='340' side='right'caption='[[1ysf]], [[NMR_Ensembles_of_Models \| 22 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ysf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YSF OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1YSF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ysf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YSF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1YSF FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ekt\|1ekt]], [[1yfb\|1yfb]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ekt\|1ekt]], [[1yfb\|1yfb]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABRB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABRB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=1ysf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ysf OCA], [http://pdbe.org/1ysf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ysf RCSB], [http://www.ebi.ac.uk/pdbsum/1ysf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ysf 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=1ysf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ysf OCA], [http://pdbe.org/1ysf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ysf RCSB], [http://www.ebi.ac.uk/pdbsum/1ysf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ysf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</StructureSection>		</StructureSection>
	[[Category: Vibrio subtilis ehrenberg 1835]]		[[Category: Vibrio subtilis ehrenberg 1835]]
		+	[[Category: Large Structures]]
	[[Category: Coles, M]]		[[Category: Coles, M]]
	[[Category: Djuranovic, S]]		[[Category: Djuranovic, S]]

OCA at 06:36, 25 April 2018

2018-04-25T06:36:20Z

←Older revision		Revision as of 06:36, 25 April 2018
Line 1:		Line 1:
		+
	==The solution structure of the N-domain of the transcription factor abrB==		==The solution structure of the N-domain of the transcription factor abrB==
	<StructureSection load='1ysf' size='340' side='right' caption='[[1ysf]], [[NMR_Ensembles_of_Models \| 22 NMR models]]' scene=''>		<StructureSection load='1ysf' size='340' side='right' caption='[[1ysf]], [[NMR_Ensembles_of_Models \| 22 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ysf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"~~bacillus_globigii~~"~~_migula_1900~~ "~~bacillus globigii~~" ~~migula 1900~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YSF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YSF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ysf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YSF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YSF FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ekt\|1ekt]], [[1yfb\|1yfb]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ekt\|1ekt]], [[1yfb\|1yfb]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABRB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "~~Bacillus globigii~~" ~~Migula 1900~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABRB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=1ysf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ysf OCA], [http://pdbe.org/1ysf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ysf RCSB], [http://www.ebi.ac.uk/pdbsum/1ysf 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=1ysf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ysf OCA], [http://pdbe.org/1ysf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ysf RCSB], [http://www.ebi.ac.uk/pdbsum/1ysf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ysf 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/ys/1ysf_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ys/1ysf_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 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus globigii migula 1900~~]]	+	[[Category: Vibrio subtilis ehrenberg 1835]]
	[[Category: Coles, M]]		[[Category: Coles, M]]
	[[Category: Djuranovic, S]]		[[Category: Djuranovic, S]]

OCA at 18:39, 9 February 2016

2016-02-09T18:39:50Z

←Older revision		Revision as of 18:39, 9 February 2016
Line 17:		Line 17:
	<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=1ysf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:58, 11 September 2015

2015-09-11T00:58:40Z

←Older revision		Revision as of 00:58, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1ysf' size='340' side='right' caption='[[1ysf]], [[NMR_Ensembles_of_Models \| 22 NMR models]]' scene=''>		<StructureSection load='1ysf' size='340' side='right' caption='[[1ysf]], [[NMR_Ensembles_of_Models \| 22 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ysf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_subtilis Bacillus subtilis~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YSF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YSF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ysf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YSF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YSF FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ekt\|1ekt]], [[1yfb\|1yfb]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ekt\|1ekt]], [[1yfb\|1yfb]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABRB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus ~~subtilis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABRB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=1ysf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ysf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ysf RCSB], [http://www.ebi.ac.uk/pdbsum/1ysf 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=1ysf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ysf OCA], [http://pdbe.org/1ysf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ysf RCSB], [http://www.ebi.ac.uk/pdbsum/1ysf 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 1ysf" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~subtilis~~]]	+	[[Category: Bacillus globigii migula 1900]]
	[[Category: Coles, M]]		[[Category: Coles, M]]
	[[Category: Djuranovic, S]]		[[Category: Djuranovic, S]]

OCA at 08:44, 25 December 2014

2014-12-25T08:44:26Z

←Older revision		Revision as of 08:44, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ysf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YSF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YSF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ysf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YSF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YSF FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ekt\|1ekt]], [[1yfb\|1yfb]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ekt\|1ekt]], [[1yfb\|1yfb]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABRB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABRB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=1ysf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ysf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ysf RCSB], [http://www.ebi.ac.uk/pdbsum/1ysf 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=1ysf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ysf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ysf RCSB], [http://www.ebi.ac.uk/pdbsum/1ysf PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ABRB_BACSU ABRB_BACSU]] Ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation. It controls the expression of genes spovG and tycA. AbrB binds to the tycA promoter region at two A- and T-rich sites, it may be the sole repressor of tycA transcription.<ref>PMID:2504584</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: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
-	[[Category: Coles, M.]]	+	[[Category: Coles, M]]
-	[[Category: Djuranovic, S.]]	+	[[Category: Djuranovic, S]]
-	[[Category: Truffault, V.]]	+	[[Category: Truffault, V]]
	[[Category: Bioinformatic]]		[[Category: Bioinformatic]]
	[[Category: Homodimer]]		[[Category: Homodimer]]

OCA at 19:56, 29 September 2014

2014-09-29T19:56:41Z

←Older revision		Revision as of 19:56, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1ysf.~~png~~\|~~left~~\|200px]]	+	==The solution structure of the N-domain of the transcription factor abrB==
		+	<StructureSection load='1ysf' size='340' side='right' caption='[[1ysf]], [[NMR_Ensembles_of_Models \| 22 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ysf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YSF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YSF FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ekt\|1ekt]], [[1yfb\|1yfb]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABRB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=1ysf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ysf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ysf RCSB], [http://www.ebi.ac.uk/pdbsum/1ysf 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/ys/1ysf_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 ==
		+	AbrB is a key transition-state regulator of Bacillus subtilis. Based on the conservation of a betaalphabeta structural unit, we proposed a beta barrel fold for its DNA binding domain, similar to, but topologically distinct from, double-psi beta barrels. However, the NMR structure revealed a novel fold, the "looped-hinge helix." To understand this discrepancy, we undertook a bioinformatics study of AbrB and its homologs; these form a large superfamily, which includes SpoVT, PrlF, MraZ, addiction module antidotes (PemI, MazE), plasmid maintenance proteins (VagC, VapB), and archaeal PhoU homologs. MazE and MraZ form swapped-hairpin beta barrels. We therefore reexamined the fold of AbrB by NMR spectroscopy and found that it also forms a swapped-hairpin barrel. The conservation of the core betaalphabeta element supports a common evolutionary origin for swapped-hairpin and double-psi barrels, which we group into a higher-order class, the cradle-loop barrels, based on the peculiar shape of their ligand binding site.

-	~~{{STRUCTURE_1ysf\| PDB=1ysf \| SCENE= }}~~	+	AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels.,Coles M, Djuranovic S, Soding J, Frickey T, Koretke K, Truffault V, Martin J, Lupas AN Structure. 2005 Jun;13(6):919-28. PMID:15939023<ref>PMID:15939023</ref>

-	~~===The solution structure~~ of the ~~N-domain of the transcription factor abrB===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15939023}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1ysf]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_subtilis Bacillus subtilis]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1YSF OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015939023<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Coles, M.]]		[[Category: Coles, M.]]

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

2013-01-05T17:14:11Z

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

←Older revision

Revision as of 17:14, 5 January 2013

OCA at 17:14, 5 January 2013

2013-01-05T17:14:07Z

←Older revision		Revision as of 17:14, 5 January 2013
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-	{{Seed}}
	[[Image:1ysf.png\|left\|200px]]		[[Image:1ysf.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1ysf", 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_1ysf\| PDB=1ysf \| SCENE= }}		{{STRUCTURE_1ysf\| PDB=1ysf \| SCENE= }}

	===The solution structure of the N-domain of the transcription factor abrB===		===The solution structure of the N-domain of the transcription factor abrB===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15939023}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15939023 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15939023}}		{{ABSTRACT_PUBMED_15939023}}

	==About this Structure==		==About this Structure==
-	~~1YSF~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YSF OCA].	+	[[1ysf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YSF OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15939023~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015939023</ref><references group="xtra"/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Coles, M.]]		[[Category: Coles, M.]]
Line 32:		Line 20:
	[[Category: Nmr]]		[[Category: Nmr]]
	[[Category: Swapped-hairpin barrel]]		[[Category: Swapped-hairpin barrel]]
-		+	[[Category: Transcription]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 11:54:35 2009''~~	+