2phe - Revision history

OCA at 09:43, 22 May 2024

2024-05-22T09:43:31Z

← Older revision		Revision as of 09:43, 22 May 2024
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	==Model for VP16 binding to PC4==		==Model for VP16 binding to PC4==
	<StructureSection load='2phe' size='340' side='right'caption='[[2phe~~]], [[NMR_Ensembles_of_Models \| 10 NMR models~~]]' scene=''>		<StructureSection load='2phe' size='340' side='right'caption='[[2phe]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2phe]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Hhv-1 Hhv-1~~] and [https://en.wikipedia.org/wiki/Human ~~Human~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PHE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PHE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2phe]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_alphaherpesvirus_1_strain_17 Human alphaherpesvirus 1 strain 17]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PHE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PHE 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;'>[[1pcf\|1pcf]], [[2phg\|2phg]]</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~~">SUB1, PC4, RPO2TC1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), UL48 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10299 HHV-1])</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=2phe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2phe OCA], [https://pdbe.org/2phe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2phe RCSB], [https://www.ebi.ac.uk/pdbsum/2phe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2phe 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=2phe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2phe OCA], [https://pdbe.org/2phe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2phe RCSB], [https://www.ebi.ac.uk/pdbsum/2phe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2phe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/TCP4_HUMAN TCP4_HUMAN]] General coactivator that functions cooperatively with TAFs and mediates functional interactions between upstream activators and the general transcriptional machinery. May be involved in stabilizing the multiprotein transcription complex. Binds single-stranded DNA. Also binds, in vitro, non-specifically to double-stranded DNA (ds DNA).<ref>PMID:8062392</ref> <ref>PMID:8062391</ref> <ref>PMID:7628453</ref> <ref>PMID:9482861</ref> <ref>PMID:16689930</ref> <ref>PMID:9360603</ref> <ref>PMID:16605275</ref> [[https://www.uniprot.org/uniprot/VP16_HHV11 VP16_HHV11]] Transcriptional activator of immediate-early (IE) gene products (alpha genes). Acts as a key activator of lytic infection by initiating the lytic program through the assembly of the transcriptional regulatory VP16-induced complex composed of VP16 and two cellular factors, HCFC1 and POU2F 1. VP16-induced complex represents a regulatory switch: when it is on, it promotes IE-gene expression and thus lytic infection, and when it is off, it limits IE-gene transcription favoring latent infection. May play a role in the aggregation of tegument proteins around nucleocapsids during virus morphogenesis.		[https://www.uniprot.org/uniprot/TCP4_HUMAN TCP4_HUMAN] General coactivator that functions cooperatively with TAFs and mediates functional interactions between upstream activators and the general transcriptional machinery. May be involved in stabilizing the multiprotein transcription complex. Binds single-stranded DNA. Also binds, in vitro, non-specifically to double-stranded DNA (ds DNA).<ref>PMID:8062392</ref> <ref>PMID:8062391</ref> <ref>PMID:7628453</ref> <ref>PMID:9482861</ref> <ref>PMID:16689930</ref> <ref>PMID:9360603</ref> <ref>PMID:16605275</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Hhv-1~~]]		[[Category: Homo sapiens]]
	[[Category: Human]]		[[Category: Human alphaherpesvirus 1 strain 17]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Boelens, R]]		[[Category: Boelens R]]
	[[Category: Folkers~~, G E~~]]		[[Category: Folkers GE]]
	[[Category: Jonker~~, H R.A~~]]		[[Category: Jonker HRA]]
	[[Category: Kaptein, R]]		[[Category: Kaptein R]]
	[[Category: Wechselberger~~, R W]]~~		[[Category: Wechselberger RW]]
	~~[[Category: Activator]]~~
	~~[[Category: Cofactor]]~~
	~~[[Category: Pc4]]~~
	~~[[Category: Transcription]]~~
	~~[[Category: Vp16~~]]

OCA at 15:24, 17 June 2021

2021-06-17T15:24:21Z

← Older revision		Revision as of 15:24, 17 June 2021
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	==Model for VP16 binding to PC4==		==Model for VP16 binding to PC4==
	<StructureSection load='2phe' size='340' side='right' caption='[[2phe]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2phe' size='340' side='right'caption='[[2phe]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2phe]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Hhv-1 Hhv-1] and [~~http~~://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PHE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PHE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2phe]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Hhv-1 Hhv-1] and [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PHE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PHE FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pcf\|1pcf]], [[2phg\|2phg]]</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;'>[[1pcf\|1pcf]], [[2phg\|2phg]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUB1, PC4, RPO2TC1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), UL48 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10299 HHV-1])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUB1, PC4, RPO2TC1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), UL48 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10299 HHV-1])</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=2phe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2phe OCA], [~~http~~://pdbe.org/2phe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2phe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2phe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2phe 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=2phe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2phe OCA], [https://pdbe.org/2phe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2phe RCSB], [https://www.ebi.ac.uk/pdbsum/2phe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2phe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/TCP4_HUMAN TCP4_HUMAN]] General coactivator that functions cooperatively with TAFs and mediates functional interactions between upstream activators and the general transcriptional machinery. May be involved in stabilizing the multiprotein transcription complex. Binds single-stranded DNA. Also binds, in vitro, non-specifically to double-stranded DNA (ds DNA).<ref>PMID:8062392</ref> <ref>PMID:8062391</ref> <ref>PMID:7628453</ref> <ref>PMID:9482861</ref> <ref>PMID:16689930</ref> <ref>PMID:9360603</ref> <ref>PMID:16605275</ref> [[~~http~~://www.uniprot.org/uniprot/VP16_HHV11 VP16_HHV11]] Transcriptional activator of immediate-early (IE) gene products (alpha genes). Acts as a key activator of lytic infection by initiating the lytic program through the assembly of the transcriptional regulatory VP16-induced complex composed of VP16 and two cellular factors, HCFC1 and POU2F 1. VP16-induced complex represents a regulatory switch: when it is on, it promotes IE-gene expression and thus lytic infection, and when it is off, it limits IE-gene transcription favoring latent infection. May play a role in the aggregation of tegument proteins around nucleocapsids during virus morphogenesis.		[[https://www.uniprot.org/uniprot/TCP4_HUMAN TCP4_HUMAN]] General coactivator that functions cooperatively with TAFs and mediates functional interactions between upstream activators and the general transcriptional machinery. May be involved in stabilizing the multiprotein transcription complex. Binds single-stranded DNA. Also binds, in vitro, non-specifically to double-stranded DNA (ds DNA).<ref>PMID:8062392</ref> <ref>PMID:8062391</ref> <ref>PMID:7628453</ref> <ref>PMID:9482861</ref> <ref>PMID:16689930</ref> <ref>PMID:9360603</ref> <ref>PMID:16605275</ref> [[https://www.uniprot.org/uniprot/VP16_HHV11 VP16_HHV11]] Transcriptional activator of immediate-early (IE) gene products (alpha genes). Acts as a key activator of lytic infection by initiating the lytic program through the assembly of the transcriptional regulatory VP16-induced complex composed of VP16 and two cellular factors, HCFC1 and POU2F 1. VP16-induced complex represents a regulatory switch: when it is on, it promotes IE-gene expression and thus lytic infection, and when it is off, it limits IE-gene transcription favoring latent infection. May play a role in the aggregation of tegument proteins around nucleocapsids during virus morphogenesis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: Hhv-1]]		[[Category: Hhv-1]]
	[[Category: Human]]		[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Boelens, R]]		[[Category: Boelens, R]]
	[[Category: Folkers, G E]]		[[Category: Folkers, G E]]

OCA at 08:37, 29 August 2018

2018-08-29T08:37:21Z

← Older revision		Revision as of 08:37, 29 August 2018
Line 1:		Line 1:

	==Model for VP16 binding to PC4==		==Model for VP16 binding to PC4==
	<StructureSection load='2phe' size='340' side='right' caption='[[2phe]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2phe' size='340' side='right' caption='[[2phe]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
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	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pcf\|1pcf]], [[2phg\|2phg]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pcf\|1pcf]], [[2phg\|2phg]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUB1, PC4, RPO2TC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), UL48 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10299 HHV-1])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUB1, PC4, RPO2TC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), UL48 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10299 HHV-1])</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=2phe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2phe OCA], [http://pdbe.org/2phe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2phe RCSB], [http://www.ebi.ac.uk/pdbsum/2phe 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=2phe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2phe OCA], [http://pdbe.org/2phe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2phe RCSB], [http://www.ebi.ac.uk/pdbsum/2phe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2phe 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/ph/2phe_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ph/2phe_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=2phe ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 12:12, 11 September 2015

2015-09-11T12:12:23Z

← Older revision		Revision as of 12:12, 11 September 2015
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	<StructureSection load='2phe' size='340' side='right' caption='[[2phe]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2phe' size='340' side='right' caption='[[2phe]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2phe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~] and [http://en.wikipedia.org/wiki/~~Viruses Viruses~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PHE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PHE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2phe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Hhv-1 Hhv-1] and [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PHE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PHE FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pcf\|1pcf]], [[2phg\|2phg]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pcf\|1pcf]], [[2phg\|2phg]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUB1, PC4, RPO2TC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~]), UL48 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~10239 Viruses~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUB1, PC4, RPO2TC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), UL48 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10299 HHV-1])</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=2phe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2phe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2phe RCSB], [http://www.ebi.ac.uk/pdbsum/2phe 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=2phe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2phe OCA], [http://pdbe.org/2phe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2phe RCSB], [http://www.ebi.ac.uk/pdbsum/2phe PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/TCP4_HUMAN TCP4_HUMAN]] General coactivator that functions cooperatively with TAFs and mediates functional interactions between upstream activators and the general transcriptional machinery. May be involved in stabilizing the multiprotein transcription complex. Binds single-stranded DNA. Also binds, in vitro, non-specifically to double-stranded DNA (ds DNA).<ref>PMID:8062392</ref> <ref>PMID:8062391</ref> <ref>PMID:7628453</ref> <ref>PMID:9482861</ref> <ref>PMID:16689930</ref> <ref>PMID:9360603</ref> <ref>PMID:16605275</ref> [[http://www.uniprot.org/uniprot/~~ATIN_HHV11 ATIN_HHV11~~]] Transcriptional activator of immediate-early (IE) gene products (alpha genes). Acts as a key activator of lytic infection by initiating the lytic program through the assembly of the transcriptional regulatory VP16-induced complex composed of VP16 and two cellular factors, HCFC1 and POU2F 1. VP16-induced complex represents a regulatory switch: when it is on, it promotes IE-gene expression and thus lytic infection, and when it is off, it limits IE-gene transcription favoring latent infection. May play a role in the aggregation of tegument proteins around nucleocapsids during virus morphogenesis ~~(Potential)~~.		[[http://www.uniprot.org/uniprot/TCP4_HUMAN TCP4_HUMAN]] General coactivator that functions cooperatively with TAFs and mediates functional interactions between upstream activators and the general transcriptional machinery. May be involved in stabilizing the multiprotein transcription complex. Binds single-stranded DNA. Also binds, in vitro, non-specifically to double-stranded DNA (ds DNA).<ref>PMID:8062392</ref> <ref>PMID:8062391</ref> <ref>PMID:7628453</ref> <ref>PMID:9482861</ref> <ref>PMID:16689930</ref> <ref>PMID:9360603</ref> <ref>PMID:16605275</ref> [[http://www.uniprot.org/uniprot/VP16_HHV11 VP16_HHV11]] Transcriptional activator of immediate-early (IE) gene products (alpha genes). Acts as a key activator of lytic infection by initiating the lytic program through the assembly of the transcriptional regulatory VP16-induced complex composed of VP16 and two cellular factors, HCFC1 and POU2F 1. VP16-induced complex represents a regulatory switch: when it is on, it promotes IE-gene expression and thus lytic infection, and when it is off, it limits IE-gene transcription favoring latent infection. May play a role in the aggregation of tegument proteins around nucleocapsids during virus morphogenesis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	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 2phe" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Homo sapiens~~]]		[[Category: Hhv-1]]
	[[Category: ~~Viruses~~]]		[[Category: Human]]
	[[Category: Boelens, R]]		[[Category: Boelens, R]]
	[[Category: Folkers, G E]]		[[Category: Folkers, G E]]

OCA at 16:17, 25 December 2014

2014-12-25T16:17:26Z

← Older revision		Revision as of 16:17, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2phe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Viruses Viruses]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PHE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PHE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2phe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Viruses Viruses]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PHE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PHE FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pcf\|1pcf]], [[2phg\|2phg]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pcf\|1pcf]], [[2phg\|2phg]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUB1, PC4, RPO2TC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), UL48 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10239 Viruses])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUB1, PC4, RPO2TC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), UL48 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10239 Viruses])</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=2phe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2phe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2phe RCSB], [http://www.ebi.ac.uk/pdbsum/2phe 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=2phe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2phe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2phe RCSB], [http://www.ebi.ac.uk/pdbsum/2phe PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/TCP4_HUMAN TCP4_HUMAN]] General coactivator that functions cooperatively with TAFs and mediates functional interactions between upstream activators and the general transcriptional machinery. May be involved in stabilizing the multiprotein transcription complex. Binds single-stranded DNA. Also binds, in vitro, non-specifically to double-stranded DNA (ds DNA).<ref>PMID:8062392</ref> <ref>PMID:8062391</ref> <ref>PMID:7628453</ref> <ref>PMID:9482861</ref> <ref>PMID:16689930</ref> <ref>PMID:9360603</ref> <ref>PMID:16605275</ref> [[http://www.uniprot.org/uniprot/ATIN_HHV11 ATIN_HHV11]] Transcriptional activator of immediate-early (IE) gene products (alpha genes). Acts as a key activator of lytic infection by initiating the lytic program through the assembly of the transcriptional regulatory VP16-induced complex composed of VP16 and two cellular factors, HCFC1 and POU2F 1. VP16-induced complex represents a regulatory switch: when it is on, it promotes IE-gene expression and thus lytic infection, and when it is off, it limits IE-gene transcription favoring latent infection. May play a role in the aggregation of tegument proteins around nucleocapsids during virus morphogenesis (Potential).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Viruses]]		[[Category: Viruses]]
	[[Category: Boelens, R.]]		[[Category: Boelens, R]]
	[[Category: Folkers, G E.]]		[[Category: Folkers, G E]]
	[[Category: Jonker, H R.A.]]		[[Category: Jonker, H R.A]]
	[[Category: Kaptein, R.]]		[[Category: Kaptein, R]]
	[[Category: Wechselberger, R W.]]		[[Category: Wechselberger, R W]]
	[[Category: Activator]]		[[Category: Activator]]
	[[Category: Cofactor]]		[[Category: Cofactor]]

OCA at 19:25, 30 September 2014

2014-09-30T19:25:49Z

← Older revision		Revision as of 19:25, 30 September 2014
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	[[Image:~~2phe~~.~~png~~\|~~left~~\|~~200px~~]]		==Model for VP16 binding to PC4==
			<StructureSection load='2phe' size='340' side='right' caption='[[2phe]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2phe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Viruses Viruses]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PHE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PHE FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pcf\|1pcf]], [[2phg\|2phg]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUB1, PC4, RPO2TC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), UL48 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10239 Viruses])</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=2phe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2phe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2phe RCSB], [http://www.ebi.ac.uk/pdbsum/2phe 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/ph/2phe_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 ==
			Herpes simplex virion protein 16 (VP16) contains two strong activation regions that can independently and cooperatively activate transcription in vivo. We have identified the regions and residues involved in the interaction with the human transcriptional coactivator positive cofactor 4 (PC4) and the general transcription factor TFIIB. NMR and biochemical experiments revealed that both VP16 activation regions are required for the interaction and undergo a conformational transition from random coil to alpha-helix upon binding to its target PC4. The interaction is strongly electrostatically driven and the binding to PC4 is enhanced by the presence of its amino-terminal domain. We propose models for binding of VP16 to the core domains of PC4 and TFIIB that are based on two independent docking approaches using NMR chemical shift changes observed in titration experiments. The models are consistent with results from site-directed mutagenesis and provide an explanation for the contribution of both acidic and hydrophobic residues for transcriptional activation by VP16. Both intrinsically unstructured activation domains are attracted to their interaction partner by electrostatic interactions, and adopt an alpha-helical conformation around the important hydrophobic residues. The models showed multiple distinct binding surfaces upon interaction with various partners, providing an explanation for the promiscuous properties, cooperativity, and the high activity of this activation domain.

	~~{{STRUCTURE_2phe\| PDB=2phe \| SCENE= }}~~		Structural properties of the promiscuous VP16 activation domain.,Jonker HR, Wechselberger RW, Boelens R, Folkers GE, Kaptein R Biochemistry. 2005 Jan 25;44(3):827-39. PMID:15654739<ref>PMID:15654739</ref>

	~~===Model for VP16 binding to PC4===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_15654739}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2phe]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens] and [http://en~~.~~wikipedia.org~~/~~wiki/Viruses Viruses]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PHE OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:015654739<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Viruses]]		[[Category: Viruses]]

OCA: Protected "2phe" [edit=sysop:move=sysop]

2013-01-07T11:46:12Z

Protected "2phe" [edit=sysop:move=sysop]

← Older revision	Revision as of 11:46, 7 January 2013
(No difference)

OCA at 11:46, 7 January 2013

2013-01-07T11:46:10Z

← Older revision		Revision as of 11:46, 7 January 2013
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	~~{{Seed}}~~
	[[Image:2phe.png\|left\|200px]]		[[Image:2phe.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2phe", 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_2phe\| PDB=2phe \| SCENE= }}		{{STRUCTURE_2phe\| PDB=2phe \| SCENE= }}

	===Model for VP16 binding to PC4===		===Model for VP16 binding to PC4===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_15654739}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 15654739 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_15654739}}		{{ABSTRACT_PUBMED_15654739}}

	==About this Structure==		==About this Structure==
	~~2PHE~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/~~Human_herpesvirus_1 Human herpesvirus 1~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PHE OCA].		[[2phe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Viruses Viruses]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PHE OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~15654739~~</ref><references group="xtra"/>		<ref group="xtra">PMID:015654739</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: ~~Human herpesvirus 1~~]]		[[Category: Viruses]]
	[[Category: Boelens, R.]]		[[Category: Boelens, R.]]
	[[Category: Folkers, G E.]]		[[Category: Folkers, G E.]]
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	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Vp16]]		[[Category: Vp16]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:31:57 2009''~~

OCA at 19:31, 17 February 2009

2009-02-17T19:31:57Z

← Older revision		Revision as of 19:31, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	2PHE is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_herpesvirus_1 Human herpesvirus 1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PHE OCA].		2PHE is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_herpesvirus_1 Human herpesvirus 1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PHE OCA].

	==Reference==		==Reference==
	~~Structural properties of the promiscuous VP16 activation domain., Jonker HR, Wechselberger RW, Boelens R, Folkers GE, Kaptein R, Biochemistry. 2005 Jan 25;44(3):827-39.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15654739 15654739]~~		<ref group="xtra">PMID:15654739</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Human herpesvirus 1]]		[[Category: Human herpesvirus 1]]
	~~[[Category: Protein complex]]~~
	[[Category: Boelens, R.]]		[[Category: Boelens, R.]]
	[[Category: Folkers, G E.]]		[[Category: Folkers, G E.]]
Line 38:		Line 37:
	[[Category: Vp16]]		[[Category: Vp16]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 05~~:39:~~09 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:31:57 2009''

OCA at 02:39, 29 July 2008

2008-07-29T02:39:16Z

← Older revision		Revision as of 02:39, 29 July 2008
Line 1:		Line 1:
	[[Image:2phe.~~gif~~\|left\|200px]]		{{Seed}}
			[[Image:2phe.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2phe\| PDB=2phe \| SCENE= }}		{{STRUCTURE_2phe\| PDB=2phe \| SCENE= }}

	~~'''~~Model for VP16 binding to PC4~~'''~~		===Model for VP16 binding to PC4===


	~~==Overview==~~		<!--
	~~Herpes simplex virion protein 16 (VP16) contains two strong activation regions that can independently and cooperatively activate transcription in vivo. We have identified~~ the ~~regions and residues involved in~~ the ~~interaction with the human transcriptional coactivator positive cofactor 4~~ (~~PC4) and the general transcription factor TFIIB~~. NMR and biochemical experiments revealed that both VP16 activation regions are required for the interaction and undergo a conformational transition from random coil to alpha-helix upon binding to its target PC4. ~~The interaction~~ is ~~strongly electrostatically driven and~~ the ~~binding to PC4 is enhanced by the presence of its amino-terminal domain~~. We propose models for binding of VP16 to the core domains of PC4 and TFIIB that are based on two independent docking approaches using NMR chemical shift changes observed in titration experiments. The models are consistent with results from site-directed mutagenesis and provide an explanation for the contribution of both acidic and hydrophobic residues for transcriptional activation by VP16. Both intrinsically unstructured activation domains are attracted to their interaction partner by electrostatic interactions, and adopt an alpha-helical conformation around the important hydrophobic residues. The models showed multiple distinct binding surfaces upon interaction with various partners, providing an explanation for the promiscuous properties, cooperativity, and the high activity of this activation domain.		The line below this paragraph, {{ABSTRACT_PUBMED_15654739}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 15654739 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_15654739}}

	==About this Structure==		==About this Structure==
	2PHE is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_herpesvirus_1 Human herpesvirus 1]. Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PHE OCA].		2PHE is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_herpesvirus_1 Human herpesvirus 1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PHE OCA].

	==Reference==		==Reference==
Line 33:		Line 37:
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Vp16]]		[[Category: Vp16]]
	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 13~~:06:51 2008''
			''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 05:39:09 2008''