3kmz - Revision history

OCA at 08:19, 6 September 2023

2023-09-06T08:19:30Z

←Older revision		Revision as of 08:19, 6 September 2023
Line 1:		Line 1:

	==Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment==		==Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment==
-	<StructureSection load='3kmz' size='340' side='right' caption='[[3kmz]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3kmz' size='340' side='right'caption='[[3kmz]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kmz]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KMZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3KMZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kmz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KMZ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=EQO:4-{(E)-2~~-[~~5,5-DIMETHYL-8-(PHENYLETHYNYL)-5,6-DIHYDRONAPHTHALEN-~~2~~-YL]ETHENYL}BENZOIC+ACID'>EQO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.1Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=EQO:4-{(E)-2-[5,5-DIMETHYL-8-(PHENYLETHYNYL)-5,6-DIHYDRONAPHTHALEN-2-YL]ETHENYL}BENZOIC+ACID'>EQO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">NR1B1, RARA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=3kmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kmz OCA], [https://pdbe.org/3kmz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kmz RCSB], [https://www.ebi.ac.uk/pdbsum/3kmz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kmz ProSAT]</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=3kmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kmz OCA], [~~http~~://pdbe.org/3kmz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3kmz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3kmz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3kmz ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/RARA_HUMAN RARA_HUMAN]] Note=Chromosomal aberrations involving RARA are commonly found in acute promyelocytic leukemia. Translocation t(11;17)(q32;q21) with ZBTB16/PLZF; translocation t(15;17)(q21;q21) with PML; translocation t(5;17)(q32;q11) with NPM. The PML-RARA oncoprotein requires both the PML ring structure and coiled-coil domain for both interaction with UBE2I, nuclear microspeckle location and sumoylation. In addition, the coiled-coil domain functions in blocking RA-mediated transactivation and cell differentiation.	+	[https://www.uniprot.org/uniprot/RARA_HUMAN RARA_HUMAN] Note=Chromosomal aberrations involving RARA are commonly found in acute promyelocytic leukemia. Translocation t(11;17)(q32;q21) with ZBTB16/PLZF; translocation t(15;17)(q21;q21) with PML; translocation t(5;17)(q32;q11) with NPM. The PML-RARA oncoprotein requires both the PML ring structure and coiled-coil domain for both interaction with UBE2I, nuclear microspeckle location and sumoylation. In addition, the coiled-coil domain functions in blocking RA-mediated transactivation and cell differentiation.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RARA_HUMAN RARA_HUMAN]] Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation, chromatin condensation and transcriptional suppression. On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation. RARA plays an essential role in the regulation of retinoic acid-induced germ cell development during spermatogenesis. Has a role in the survival of early spermatocytes at the beginning prophase of meiosis. In Sertoli cells, may promote the survival and development of early meiotic prophase spermatocytes. In concert with RARG, required for skeletal growth, matrix homeostasis and growth plate function (By similarity). Regulates expression of target genes in a ligand-dependent manner by recruiting chromatin complexes containing MLL5. Mediates retinoic acid-induced granulopoiesis.<ref>PMID:16417524</ref> <ref>PMID:19850744</ref> <ref>PMID:19377461</ref> <ref>PMID:20215566</ref> [[http://www.uniprot.org/uniprot/NCOR1_HUMAN NCOR1_HUMAN]] Mediates transcriptional repression by certain nuclear receptors. Part of a complex which promotes histone deacetylation and the formation of repressive chromatin structures which may impede the access of basal transcription factors.<ref>PMID:14527417</ref>	+	[https://www.uniprot.org/uniprot/RARA_HUMAN RARA_HUMAN] Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation, chromatin condensation and transcriptional suppression. On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation. RARA plays an essential role in the regulation of retinoic acid-induced germ cell development during spermatogenesis. Has a role in the survival of early spermatocytes at the beginning prophase of meiosis. In Sertoli cells, may promote the survival and development of early meiotic prophase spermatocytes. In concert with RARG, required for skeletal growth, matrix homeostasis and growth plate function (By similarity). Regulates expression of target genes in a ligand-dependent manner by recruiting chromatin complexes containing MLL5. Mediates retinoic acid-induced granulopoiesis.<ref>PMID:16417524</ref> <ref>PMID:19850744</ref> <ref>PMID:19377461</ref> <ref>PMID:20215566</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
	*[[Nuclear receptor corepressor\|Nuclear receptor corepressor]]		*[[Nuclear receptor corepressor\|Nuclear receptor corepressor]]
-	*[[Retinoic acid receptor\|Retinoic acid receptor]]	+	*[[Retinoic acid receptor 3D structures\|Retinoic acid receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Bourguet, W~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Maire, A le~~]]	+	[[Category: Bourguet W]]
-	[[Category: ~~Chromatin regulator]]~~	+	[[Category: Le Maire A]]
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Nuclear receptor transcription factor ligand binding domain]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Proto-oncogene]]~~	+
-	~~[[Category: Receptor]]~~	+
-	~~[[Category: Repressor]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Zinc-finger~~]]	+

OCA at 09:34, 26 December 2018

2018-12-26T09:34:40Z

←Older revision		Revision as of 09:34, 26 December 2018
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/km/3kmz_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/km/3kmz_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 34:		Line 34:

	==See Also==		==See Also==
		+	*[[Nuclear receptor corepressor\|Nuclear receptor corepressor]]
	*[[Retinoic acid receptor\|Retinoic acid receptor]]		*[[Retinoic acid receptor\|Retinoic acid receptor]]
	== References ==		== References ==

OCA at 08:52, 5 August 2016

2016-08-05T08:52:56Z

←Older revision		Revision as of 08:52, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment==		==Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment==
	<StructureSection load='3kmz' size='340' side='right' caption='[[3kmz]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3kmz' size='340' side='right' caption='[[3kmz]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kmz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KMZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kmz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KMZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EQO:4-{(E)-2-[5,5-DIMETHYL-8-(PHENYLETHYNYL)-5,6-DIHYDRONAPHTHALEN-2-YL]ETHENYL}BENZOIC+ACID'>EQO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EQO:4-{(E)-2-[5,5-DIMETHYL-8-(PHENYLETHYNYL)-5,6-DIHYDRONAPHTHALEN-2-YL]ETHENYL}BENZOIC+ACID'>EQO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NR1B1, RARA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NR1B1, RARA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3kmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kmz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kmz RCSB], [http://www.ebi.ac.uk/pdbsum/3kmz 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=3kmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kmz OCA], [http://pdbe.org/3kmz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kmz RCSB], [http://www.ebi.ac.uk/pdbsum/3kmz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kmz ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
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	<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=3kmz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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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 3kmz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 39:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Bourguet, W]]		[[Category: Bourguet, W]]
	[[Category: Maire, A le]]		[[Category: Maire, A le]]

OCA at 15:28, 18 December 2014

2014-12-18T15:28:49Z

←Older revision		Revision as of 15:28, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3kmz\| PDB=3kmz \| SCENE= }}~~	+	==Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment==
-	===Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment===	+	<StructureSection load='3kmz' size='340' side='right' caption='[[3kmz]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	{~~{ABSTRACT_PUBMED_20543827}~~}	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[3kmz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KMZ FirstGlance]. <br>
-	==Disease==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EQO:4-{(E)-2-[5,5-DIMETHYL-8-(PHENYLETHYNYL)-5,6-DIHYDRONAPHTHALEN-2-YL]ETHENYL}BENZOIC+ACID'>EQO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NR1B1, RARA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3kmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kmz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kmz RCSB], [http://www.ebi.ac.uk/pdbsum/3kmz PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
	[[http://www.uniprot.org/uniprot/RARA_HUMAN RARA_HUMAN]] Note=Chromosomal aberrations involving RARA are commonly found in acute promyelocytic leukemia. Translocation t(11;17)(q32;q21) with ZBTB16/PLZF; translocation t(15;17)(q21;q21) with PML; translocation t(5;17)(q32;q11) with NPM. The PML-RARA oncoprotein requires both the PML ring structure and coiled-coil domain for both interaction with UBE2I, nuclear microspeckle location and sumoylation. In addition, the coiled-coil domain functions in blocking RA-mediated transactivation and cell differentiation.		[[http://www.uniprot.org/uniprot/RARA_HUMAN RARA_HUMAN]] Note=Chromosomal aberrations involving RARA are commonly found in acute promyelocytic leukemia. Translocation t(11;17)(q32;q21) with ZBTB16/PLZF; translocation t(15;17)(q21;q21) with PML; translocation t(5;17)(q32;q11) with NPM. The PML-RARA oncoprotein requires both the PML ring structure and coiled-coil domain for both interaction with UBE2I, nuclear microspeckle location and sumoylation. In addition, the coiled-coil domain functions in blocking RA-mediated transactivation and cell differentiation.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RARA_HUMAN RARA_HUMAN]] Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation, chromatin condensation and transcriptional suppression. On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation. RARA plays an essential role in the regulation of retinoic acid-induced germ cell development during spermatogenesis. Has a role in the survival of early spermatocytes at the beginning prophase of meiosis. In Sertoli cells, may promote the survival and development of early meiotic prophase spermatocytes. In concert with RARG, required for skeletal growth, matrix homeostasis and growth plate function (By similarity). Regulates expression of target genes in a ligand-dependent manner by recruiting chromatin complexes containing MLL5. Mediates retinoic acid-induced granulopoiesis.<ref>PMID:16417524</ref> <ref>PMID:19850744</ref> <ref>PMID:19377461</ref> <ref>PMID:20215566</ref> [[http://www.uniprot.org/uniprot/NCOR1_HUMAN NCOR1_HUMAN]] Mediates transcriptional repression by certain nuclear receptors. Part of a complex which promotes histone deacetylation and the formation of repressive chromatin structures which may impede the access of basal transcription factors.<ref>PMID:14527417</ref>
		+	== 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/km/3kmz_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 ==
		+	In the absence of ligand, some nuclear receptors, including retinoic acid receptor (RAR), act as transcriptional repressors by recruiting corepressor complexes to target genes. This constitutive repression is crucial in metazoan reproduction, development and homeostasis. However, its specific molecular determinants had remained obscure. Using structural, biochemical and cell-based assays, we show that the basal repressive activity of RAR is conferred by an extended beta-strand that forms an antiparallel beta-sheet with specific corepressor residues. Agonist binding induces a beta-strand-to-alpha-helix transition that allows for helix H11 formation, which in turn provokes corepressor release, repositioning of helix H12 and coactivator recruitment. Several lines of evidence suggest that this structural switch could be implicated in the intrinsic repressor function of other nuclear receptors. Finally, we report on the molecular mechanism by which inverse agonists strengthen corepressor interaction and enhance gene silencing by RAR.

-	~~==Function==~~	+	A unique secondary-structure switch controls constitutive gene repression by retinoic acid receptor.,le Maire A, Teyssier C, Erb C, Grimaldi M, Alvarez S, de Lera AR, Balaguer P, Gronemeyer H, Royer CA, Germain P, Bourguet W Nat Struct Mol Biol. 2010 Jul;17(7):801-7. Epub 2010 Jun 13. PMID:20543827<ref>PMID:20543827</ref>
-	~~[[http://www.uniprot.org/uniprot/RARA_HUMAN RARA_HUMAN]] Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all~~-~~trans or 9-cis retinoic acid, and regulate~~ gene ~~expression in various biological processes. The RXR/RAR heterodimers bind to the~~ retinoic acid ~~response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5~~. ~~In the absence of ligand~~, ~~the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation~~, ~~chromatin condensation and transcriptional suppression. On ligand binding~~, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation. RARA plays an essential role in the regulation of retinoic acid-induced germ cell development during spermatogenesis. Has a role in the survival of early spermatocytes at the beginning prophase of meiosis. In Sertoli cells, ~~may promote the survival and development of early meiotic prophase spermatocytes. In concert with RARG~~, ~~required for skeletal growth~~, ~~matrix homeostasis and growth plate function~~ (~~By similarity~~)~~. Regulates expression of target genes in a ligand~~-~~dependent manner by recruiting chromatin complexes containing MLL5~~. ~~Mediates retinoic acid-induced granulopoiesis~~.~~<ref>~~PMID:16417524</ref><ref>PMID:19850744</ref><ref>PMID:19377461</ref><ref>PMID:20215566</ref> [[http://www.uniprot.org/uniprot/NCOR1_HUMAN NCOR1_HUMAN]] Mediates transcriptional repression by certain nuclear receptors. Part of a complex which promotes histone deacetylation and the formation of repressive chromatin structures which may impede the access of basal transcription factors.<ref>PMID:~~14527417~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3kmz]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3KMZ OCA].~~	+	</div>

	==See Also==		==See Also==
	*[[Retinoic acid receptor\|Retinoic acid receptor]]		*[[Retinoic acid receptor\|Retinoic acid receptor]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:020543827</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Bourguet, W.]]	+	[[Category: Bourguet, W]]
-	[[Category: Maire, A le.]]	+	[[Category: Maire, A le]]
	[[Category: Chromatin regulator]]		[[Category: Chromatin regulator]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]

OCA at 18:58, 24 March 2013

2013-03-24T18:58:10Z

←Older revision		Revision as of 18:58, 24 March 2013
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-	[[Image:3kmz.png\|left\|200px]]
-
	{{STRUCTURE_3kmz\| PDB=3kmz \| SCENE= }}		{{STRUCTURE_3kmz\| PDB=3kmz \| SCENE= }}
-
	===Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment===		===Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment===
		+	{{ABSTRACT_PUBMED_20543827}}

-	~~{{ABSTRACT_PUBMED_20543827}}~~	+	==Disease==
		+	[[http://www.uniprot.org/uniprot/RARA_HUMAN RARA_HUMAN]] Note=Chromosomal aberrations involving RARA are commonly found in acute promyelocytic leukemia. Translocation t(11;17)(q32;q21) with ZBTB16/PLZF; translocation t(15;17)(q21;q21) with PML; translocation t(5;17)(q32;q11) with NPM. The PML-RARA oncoprotein requires both the PML ring structure and coiled-coil domain for both interaction with UBE2I, nuclear microspeckle location and sumoylation. In addition, the coiled-coil domain functions in blocking RA-mediated transactivation and cell differentiation.
		+
		+	==Function==
		+	[[http://www.uniprot.org/uniprot/RARA_HUMAN RARA_HUMAN]] Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation, chromatin condensation and transcriptional suppression. On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation. RARA plays an essential role in the regulation of retinoic acid-induced germ cell development during spermatogenesis. Has a role in the survival of early spermatocytes at the beginning prophase of meiosis. In Sertoli cells, may promote the survival and development of early meiotic prophase spermatocytes. In concert with RARG, required for skeletal growth, matrix homeostasis and growth plate function (By similarity). Regulates expression of target genes in a ligand-dependent manner by recruiting chromatin complexes containing MLL5. Mediates retinoic acid-induced granulopoiesis.<ref>PMID:16417524</ref><ref>PMID:19850744</ref><ref>PMID:19377461</ref><ref>PMID:20215566</ref> [[http://www.uniprot.org/uniprot/NCOR1_HUMAN NCOR1_HUMAN]] Mediates transcriptional repression by certain nuclear receptors. Part of a complex which promotes histone deacetylation and the formation of repressive chromatin structures which may impede the access of basal transcription factors.<ref>PMID:14527417</ref>

	==About this Structure==		==About this Structure==
Line 14:		Line 16:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:020543827</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020543827</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Bourguet, W.]]		[[Category: Bourguet, W.]]

OCA: Protected "3kmz" [edit=sysop:move=sysop]

2012-10-20T10:52:54Z

Protected "3kmz" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:52, 20 October 2012

OCA at 10:52, 20 October 2012

2012-10-20T10:52:52Z

←Older revision		Revision as of 10:52, 20 October 2012
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-	{{Seed}}
	[[Image:3kmz.png\|left\|200px]]		[[Image:3kmz.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3kmz", 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_3kmz\| PDB=3kmz \| SCENE= }}		{{STRUCTURE_3kmz\| PDB=3kmz \| SCENE= }}

	===Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment===		===Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20543827}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20543827 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20543827}}		{{ABSTRACT_PUBMED_20543827}}

	==About this Structure==		==About this Structure==
-	~~3KMZ~~ is a 4 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KMZ OCA].	+	[[3kmz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KMZ OCA].
		+
		+	==See Also==
		+	*[[Retinoic acid receptor\|Retinoic acid receptor]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20543827~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020543827</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Bourguet, W.]]		[[Category: Bourguet, W.]]
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	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 14 15:58:37 2010''

OCA at 11:52, 14 July 2010

2010-07-14T11:52:28Z

←Older revision		Revision as of 11:52, 14 July 2010
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	[[Category: Bourguet, W.]]		[[Category: Bourguet, W.]]
	[[Category: Maire, A le.]]		[[Category: Maire, A le.]]
-	[[Category: Acetylation]]
-	[[Category: Alternative splicing]]
	[[Category: Chromatin regulator]]		[[Category: Chromatin regulator]]
-	[[Category: Chromosomal rearrangement]]
-	[[Category: Coiled coil]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
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	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
-	[[Category: Ubl conjugation]]
-	[[Category: Zinc]]
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jun 23 08~~:39:10 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 14 15:58:37 2010''

OCA at 04:33, 23 June 2010

2010-06-23T04:33:52Z

←Older revision		Revision as of 04:33, 23 June 2010
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	{{Seed}}		{{Seed}}
-	[[Image:3kmz.~~jpg~~\|left\|200px]]	+	[[Image:3kmz.png\|left\|200px]]

	<!--		<!--
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	===Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment===		===Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20543827}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20543827 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20543827}}

	==About this Structure==		==About this Structure==
	3KMZ is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KMZ OCA].		3KMZ is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KMZ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20543827</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Bourguet, W.]]		[[Category: Bourguet, W.]]
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	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 2 08:38:38 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 23 08:39:10 2010''

OCA at 04:34, 2 June 2010

2010-06-02T04:34:10Z

←Older revision		Revision as of 04:34, 2 June 2010
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3kmz.jpg\|left\|200px]]

-	The ~~entry 3kmz~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3kmz", 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_3kmz\| PDB=3kmz \| SCENE= }}

-	~~Authors: Bourguet, W., le Maire, A.~~	+	===Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment===

-	Description: Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Dec 23 09~~:22:~~49 2009~~''	+	==About this Structure==
		+	3KMZ is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KMZ OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Bourguet, W.]]
		+	[[Category: Maire, A le.]]
		+	[[Category: Acetylation]]
		+	[[Category: Alternative splicing]]
		+	[[Category: Chromatin regulator]]
		+	[[Category: Chromosomal rearrangement]]
		+	[[Category: Coiled coil]]
		+	[[Category: Dna-binding]]
		+	[[Category: Metal-binding]]
		+	[[Category: Nuclear receptor transcription factor ligand binding domain]]
		+	[[Category: Nucleus]]
		+	[[Category: Phosphoprotein]]
		+	[[Category: Proto-oncogene]]
		+	[[Category: Receptor]]
		+	[[Category: Repressor]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription regulation]]
		+	[[Category: Ubl conjugation]]
		+	[[Category: Zinc]]
		+	[[Category: Zinc-finger]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 2 08:38:38 2010''