3a2h - Revision history

OCA at 14:09, 1 November 2023

OCA — Wed, 01 Nov 2023 14:09:05 GMT

←Older revision		Revision as of 14:09, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='3a2h' size='340' side='right'caption='[[3a2h]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3a2h' size='340' side='right'caption='[[3a2h]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3a2h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A2H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3a2h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A2H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TEJ:(1S,3R,5Z,7E,20S,23S)-1,3-DIHYDROXY-23,26-EPOXY-9,10-SECOCHOLESTA-5,7,10,25(27)-TETRAEN-26-ONE'>TEJ</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]] 2.5Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3a2i\|3a2i]], [[3a2j\|3a2j]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TEJ:(1S,3R,5Z,7E,20S,23S)-1,3-DIHYDROXY-23,26-EPOXY-9,10-SECOCHOLESTA-5,7,10,25(27)-TETRAEN-26-ONE'>TEJ</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vdr, Nr1i1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])~~</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=3a2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a2h OCA], [https://pdbe.org/3a2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a2h RCSB], [https://www.ebi.ac.uk/pdbsum/3a2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a2h 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=3a2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a2h OCA], [https://pdbe.org/3a2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a2h RCSB], [https://www.ebi.ac.uk/pdbsum/3a2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a2h ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/VDR_RAT VDR_RAT]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:17227670</ref> [[https://www.uniprot.org/uniprot/MED1_HUMAN MED1_HUMAN]] Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.<ref>PMID:9653119</ref> <ref>PMID:10406464</ref> <ref>PMID:12218053</ref> <ref>PMID:12037571</ref> <ref>PMID:11867769</ref> <ref>PMID:12556447</ref> <ref>PMID:14636573</ref> <ref>PMID:15471764</ref> <ref>PMID:15340084</ref> <ref>PMID:15989967</ref> <ref>PMID:16574658</ref>	+	[https://www.uniprot.org/uniprot/VDR_RAT VDR_RAT] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:17227670</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Buffalo rat~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Kakuda, S~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: ~~Takimoto-Kamimura, M~~]]	+	[[Category: Kakuda S]]
-	[[Category: ~~Activator]]~~	+	[[Category: Takimoto-Kamimura M]]
-	~~[[Category: Dna~~-~~binding]]~~	+
-	~~[[Category: Hormone receptor]]~~	+
-	~~[[Category: Hormone/growth factor receptor]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Receptor]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Zinc-finger~~]]	+

OCA at 16:15, 22 December 2021

OCA — Wed, 22 Dec 2021 16:15:26 GMT

←Older revision		Revision as of 16:15, 22 December 2021
Line 1:		Line 1:

	==Crystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205==		==Crystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205==
-	<StructureSection load='3a2h' size='340' side='right' caption='[[3a2h]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='3a2h' size='340' side='right'caption='[[3a2h]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3a2h]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A2H OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3A2H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3a2h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A2H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TEJ:(1S,3R,5Z,7E,20S,23S)-1,3-DIHYDROXY-23,26-EPOXY-9,10-SECOCHOLESTA-5,7,10,25(27)-TETRAEN-26-ONE'>TEJ</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TEJ:(1S,3R,5Z,7E,20S,23S)-1,3-DIHYDROXY-23,26-EPOXY-9,10-SECOCHOLESTA-5,7,10,25(27)-TETRAEN-26-ONE'>TEJ</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a2i\|3a2i]], [[3a2j\|3a2j]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3a2i\|3a2i]], [[3a2j\|3a2j]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vdr, Nr1i1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vdr, Nr1i1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=3a2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a2h OCA], [~~http~~://pdbe.org/3a2h PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3a2h RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3a2h PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3a2h 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=3a2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a2h OCA], [https://pdbe.org/3a2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a2h RCSB], [https://www.ebi.ac.uk/pdbsum/3a2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a2h ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/VDR_RAT VDR_RAT]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:17227670</ref> [[~~http~~://www.uniprot.org/uniprot/MED1_HUMAN MED1_HUMAN]] Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.<ref>PMID:9653119</ref> <ref>PMID:10406464</ref> <ref>PMID:12218053</ref> <ref>PMID:12037571</ref> <ref>PMID:11867769</ref> <ref>PMID:12556447</ref> <ref>PMID:14636573</ref> <ref>PMID:15471764</ref> <ref>PMID:15340084</ref> <ref>PMID:15989967</ref> <ref>PMID:16574658</ref>	+	[[https://www.uniprot.org/uniprot/VDR_RAT VDR_RAT]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:17227670</ref> [[https://www.uniprot.org/uniprot/MED1_HUMAN MED1_HUMAN]] Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.<ref>PMID:9653119</ref> <ref>PMID:10406464</ref> <ref>PMID:12218053</ref> <ref>PMID:12037571</ref> <ref>PMID:11867769</ref> <ref>PMID:12556447</ref> <ref>PMID:14636573</ref> <ref>PMID:15471764</ref> <ref>PMID:15340084</ref> <ref>PMID:15989967</ref> <ref>PMID:16574658</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a2/3a2h_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a2/3a2h_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 33:		Line 33:
	==See Also==		==See Also==
	*[[Sandbox vdr\|Sandbox vdr]]		*[[Sandbox vdr\|Sandbox vdr]]
-	*[[Vitamin D receptor\|Vitamin D receptor]]	+	*[[Vitamin D receptor 3D structures\|Vitamin D receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
		+	[[Category: Large Structures]]
	[[Category: Kakuda, S]]		[[Category: Kakuda, S]]
	[[Category: Takimoto-Kamimura, M]]		[[Category: Takimoto-Kamimura, M]]

OCA at 10:17, 5 August 2016

OCA — Fri, 05 Aug 2016 10:17:33 GMT

←Older revision		Revision as of 10:17, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205==		==Crystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205==
	<StructureSection load='3a2h' size='340' side='right' caption='[[3a2h]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3a2h' size='340' side='right' caption='[[3a2h]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3a2h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rattus_norvegicus Rattus norvegicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A2H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3A2H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3a2h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A2H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3A2H FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TEJ:(1S,3R,5Z,7E,20S,23S)-1,3-DIHYDROXY-23,26-EPOXY-9,10-SECOCHOLESTA-5,7,10,25(27)-TETRAEN-26-ONE'>TEJ</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TEJ:(1S,3R,5Z,7E,20S,23S)-1,3-DIHYDROXY-23,26-EPOXY-9,10-SECOCHOLESTA-5,7,10,25(27)-TETRAEN-26-ONE'>TEJ</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a2i\|3a2i]], [[3a2j\|3a2j]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a2i\|3a2i]], [[3a2j\|3a2j]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vdr, Nr1i1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 ~~Rattus norvegicus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vdr, Nr1i1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=3a2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a2h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3a2h RCSB], [http://www.ebi.ac.uk/pdbsum/3a2h 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=3a2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a2h OCA], [http://pdbe.org/3a2h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3a2h RCSB], [http://www.ebi.ac.uk/pdbsum/3a2h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3a2h ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3a2h ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 29:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3a2h" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rattus norvegicus~~]]	+	[[Category: Buffalo rat]]
	[[Category: Kakuda, S]]		[[Category: Kakuda, S]]
	[[Category: Takimoto-Kamimura, M]]		[[Category: Takimoto-Kamimura, M]]

OCA at 17:59, 25 December 2014

OCA — Thu, 25 Dec 2014 17:59:01 GMT

←Older revision		Revision as of 17:59, 25 December 2014
Line 8:		Line 8:
	<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=3a2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a2h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3a2h RCSB], [http://www.ebi.ac.uk/pdbsum/3a2h 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=3a2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a2h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3a2h RCSB], [http://www.ebi.ac.uk/pdbsum/3a2h PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VDR_RAT VDR_RAT]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:17227670</ref> [[http://www.uniprot.org/uniprot/MED1_HUMAN MED1_HUMAN]] Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.<ref>PMID:9653119</ref> <ref>PMID:10406464</ref> <ref>PMID:12218053</ref> <ref>PMID:12037571</ref> <ref>PMID:11867769</ref> <ref>PMID:12556447</ref> <ref>PMID:14636573</ref> <ref>PMID:15471764</ref> <ref>PMID:15340084</ref> <ref>PMID:15989967</ref> <ref>PMID:16574658</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 26:		Line 28:
	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>
		+
		+	==See Also==
		+	*[[Sandbox vdr\|Sandbox vdr]]
		+	*[[Vitamin D receptor\|Vitamin D receptor]]
	== References ==		== References ==
	<references/>		<references/>
Line 31:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: Kakuda, S.]]	+	[[Category: Kakuda, S]]
-	[[Category: Takimoto-Kamimura, M.]]	+	[[Category: Takimoto-Kamimura, M]]
	[[Category: Activator]]		[[Category: Activator]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]

OCA at 12:01, 29 October 2014

OCA — Wed, 29 Oct 2014 12:01:31 GMT

←Older revision		Revision as of 12:01, 29 October 2014
Line 1:		Line 1:
-	[[~~Image:~~3a2h.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205==
		+	<StructureSection load='3a2h' size='340' side='right' caption='[[3a2h]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3a2h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A2H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3A2H FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TEJ:(1S,3R,5Z,7E,20S,23S)-1,3-DIHYDROXY-23,26-EPOXY-9,10-SECOCHOLESTA-5,7,10,25(27)-TETRAEN-26-ONE'>TEJ</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a2i\|3a2i]], [[3a2j\|3a2j]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vdr, Nr1i1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</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=3a2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a2h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3a2h RCSB], [http://www.ebi.ac.uk/pdbsum/3a2h 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/a2/3a2h_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 ==
		+	TEI-9647 antagonizes vitamin D receptor (VDR) mediated genomic actions of 1alpha,25(OH)2D3 in human cells but is agonistic in rodent cells. The presence of Cys403, Cys410 or of both residues in the C-terminal region of human VDR (hVDR) results in antagonistic action of this compound. In the complexes of TEI-9647 with wild-type hVDR (hVDRwt) and H397F hVDR, TEI-9647 functions as an antagonist and forms a covalent adduct with hVDR according to MALDI-TOF MS. The crystal structures of complexes of TEI-9647 with rat VDR (rVDR), H305F hVDR and H305F/H397F hVDR showed that the agonistic activity of TEI-9647 is caused by a hydrogen-bond interaction with His397 or Phe397 located in helix 11. Both biological activity assays and the crystal structure of H305F hVDR complexed with TEI-9647 showed that the interaction between His305 and TEI-9647 is crucial for antagonist activity. This study indicates the following stepwise mechanism for TEI-9647 antagonism. Firstly, TEI-9647 forms hydrogen bonds to His305, which promote conformational changes in hVDR and draw Cys403 or Cys410 towards the ligand. This is followed by the formation of a 1,4-Michael addition adduct between the thiol (-SH) group of Cys403 or Cys410 and the exo-methylene group of TEI-9647.

-	~~{{STRUCTURE_3a2h\| PDB=3a2h \| SCENE= }}~~	+	Structural basis of the histidine-mediated vitamin D receptor agonistic and antagonistic mechanisms of (23S)-25-dehydro-1alpha-hydroxyvitamin D3-26,23-lactone.,Kakuda S, Ishizuka S, Eguchi H, Mizwicki MT, Norman AW, Takimoto-Kamimura M Acta Crystallogr D Biol Crystallogr. 2010 Aug;66(Pt 8):918-26. Epub 2010, Jul 10. PMID:20693691<ref>PMID:20693691</ref>

-	~~===Crystal structure~~ of the ~~rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20693691}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3a2h]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rattus_norvegicus Rattus norvegicus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3A2H OCA].~~	+	</StructureSection>
-		+
-	==~~See Also==~~	+
-	*[[Vitamin D receptor\|Vitamin D receptor]]	+
-		+
-	~~==Reference~~==	+
-	<~~ref group="xtra">PMID:020693691<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Kakuda, S.]]		[[Category: Kakuda, S.]]

OCA: Protected "3a2h" [edit=sysop:move=sysop]

OCA — Sat, 20 Oct 2012 19:43:26 GMT

Protected "3a2h" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:43, 20 October 2012

OCA at 19:43, 20 October 2012

OCA — Sat, 20 Oct 2012 19:43:24 GMT

←Older revision		Revision as of 19:43, 20 October 2012
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-	{{Seed}}
	[[Image:3a2h.png\|left\|200px]]		[[Image:3a2h.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3a2h", 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_3a2h\| PDB=3a2h \| SCENE= }}		{{STRUCTURE_3a2h\| PDB=3a2h \| SCENE= }}

	===Crystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205===		===Crystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20693691}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20693691 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20693691}}		{{ABSTRACT_PUBMED_20693691}}

	==About this Structure==		==About this Structure==
-	~~3A2H~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A2H OCA].	+	[[3a2h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A2H OCA].
		+
		+	==See Also==
		+	*[[Vitamin D receptor\|Vitamin D receptor]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20693691~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020693691</ref><references group="xtra"/>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Kakuda, S.]]		[[Category: Kakuda, S.]]
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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 Aug 18 11:06:50 2010''

OCA at 06:59, 18 August 2010

OCA — Wed, 18 Aug 2010 06:59:17 GMT

←Older revision		Revision as of 06:59, 18 August 2010
Line 12:		Line 12:
	===Crystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205===		===Crystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20693691}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20693691 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20693691}}

	==About this Structure==		==About this Structure==
	3A2H is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A2H OCA].		3A2H is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A2H OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20693691</ref><references group="xtra"/>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Kakuda, S.]]		[[Category: Kakuda, S.]]
Line 30:		Line 39:
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jul 28 12~~:08:13 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 18 11:06:50 2010''

OCA at 08:01, 28 July 2010

OCA — Wed, 28 Jul 2010 08:01:31 GMT

←Older revision		Revision as of 08:01, 28 July 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3a2h.~~jpg~~\|left\|200px]]	+	[[Image:3a2h.png\|left\|200px]]

	<!--		<!--
Line 19:		Line 19:
	[[Category: Takimoto-Kamimura, M.]]		[[Category: Takimoto-Kamimura, M.]]
	[[Category: Activator]]		[[Category: Activator]]
-	[[Category: Alternative splicing]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]
	[[Category: Hormone receptor]]		[[Category: Hormone receptor]]
Line 26:		Line 25:
	[[Category: Nucleus]]		[[Category: Nucleus]]
	[[Category: Phosphoprotein]]		[[Category: Phosphoprotein]]
-	[[Category: Polymorphism]]
	[[Category: Receptor]]		[[Category: Receptor]]
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
-	[[Category: Zinc]]
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~May 26 08~~:29:37 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 28 12:08:13 2010''

OCA at 04:25, 26 May 2010

OCA — Wed, 26 May 2010 04:25:26 GMT

←Older revision		Revision as of 04:25, 26 May 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3a2h.jpg\|left\|200px]]

-	The ~~entry 3a2h~~ is ~~ON HOLD~~ ~~until May 20 2011~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3a2h", 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_3a2h\| PDB=3a2h \| SCENE= }}

-	~~Authors: Kakuda, S., Takimoto~~-~~Kamimura, M.~~	+	===Crystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205===

-	Description: Crystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jun 4 07~~:16:~~58 2009~~''	+	==About this Structure==
		+	3A2H is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A2H OCA].
		+	[[Category: Rattus norvegicus]]
		+	[[Category: Kakuda, S.]]
		+	[[Category: Takimoto-Kamimura, M.]]
		+	[[Category: Activator]]
		+	[[Category: Alternative splicing]]
		+	[[Category: Dna-binding]]
		+	[[Category: Hormone receptor]]
		+	[[Category: Hormone/growth factor receptor]]
		+	[[Category: Metal-binding]]
		+	[[Category: Nucleus]]
		+	[[Category: Phosphoprotein]]
		+	[[Category: Polymorphism]]
		+	[[Category: Receptor]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription regulation]]
		+	[[Category: Zinc]]
		+	[[Category: Zinc-finger]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 26 08:29:37 2010''