1rkg - Revision history

OCA at 06:05, 23 August 2023

OCA — Wed, 23 Aug 2023 06:05:23 GMT

←Older revision		Revision as of 06:05, 23 August 2023
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	<StructureSection load='1rkg' size='340' side='right'caption='[[1rkg]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1rkg' size='340' side='right'caption='[[1rkg]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rkg]] 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=1RKG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1RKG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rkg]] 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=1RKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RKG FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=VD1:5-{2~~-[~~1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE~~]~~-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-~~1~~,3-DIOL'>VD1</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]] 1.9Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;'>[~~[~~1rjk\|1rjk]~~], ~~[[1rk3\|1rk3]], [[1rkh\|1rkh]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VD1:5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIOL'>VD1</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=1rkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkg OCA], [https://pdbe.org/1rkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rkg RCSB], [https://www.ebi.ac.uk/pdbsum/1rkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rkg ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1rkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkg OCA], [~~http~~://pdbe.org/1rkg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1rkg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1rkg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1rkg 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>
	== 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: ~~Buffalo rat~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bauer, C B~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: ~~Benning, M M~~]]	+	[[Category: Bauer CB]]
-	[[Category: ~~DeLuca, H F~~]]	+	[[Category: Benning MM]]
-	[[Category: ~~Pike, J W~~]]	+	[[Category: DeLuca HF]]
-	[[Category: ~~Vanhooke, J L~~]]	+	[[Category: Pike JW]]
-	[[Category: ~~Hormone-growth factor receptor complex]]~~	+	[[Category: Vanhooke JL]]
-	~~[[Category: Nuclear receptor-coactivator interaction]]~~	+
-	~~[[Category: Nuclear receptor-ligand complex~~]]	+

OCA at 13:28, 16 December 2020

OCA — Wed, 16 Dec 2020 13:28:38 GMT

←Older revision		Revision as of 13:28, 16 December 2020
Line 1:		Line 1:

	==crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MbisP and a synthetic peptide containing the NR2 box of DRIP 205==		==crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MbisP and a synthetic peptide containing the NR2 box of DRIP 205==
-	<StructureSection load='1rkg' size='340' side='right' caption='[[1rkg]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='1rkg' size='340' side='right'caption='[[1rkg]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rkg]] 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=1RKG OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1RKG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rkg]] 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=1RKG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1RKG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=VD1:5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIOL'>VD1</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VD1:5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIOL'>VD1</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rjk\|1rjk]], [[1rk3\|1rk3]], [[1rkh\|1rkh]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1rjk\|1rjk]], [[1rk3\|1rk3]], [[1rkh\|1rkh]]</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 ([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=1rkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkg OCA], [http://pdbe.org/1rkg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rkg RCSB], [http://www.ebi.ac.uk/pdbsum/1rkg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rkg ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1rkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkg OCA], [http://pdbe.org/1rkg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rkg RCSB], [http://www.ebi.ac.uk/pdbsum/1rkg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rkg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rk/1rkg_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rk/1rkg_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 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1rkg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1rkg" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Sandbox vdr\|Sandbox vdr]]
		+	*[[Vitamin D receptor 3D structures\|Vitamin D receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
		+	[[Category: Large Structures]]
	[[Category: Bauer, C B]]		[[Category: Bauer, C B]]
	[[Category: Benning, M M]]		[[Category: Benning, M M]]

OCA at 11:48, 12 October 2017

OCA — Thu, 12 Oct 2017 11:48:31 GMT

←Older revision		Revision as of 11:48, 12 October 2017
Line 1:		Line 1:
		+
	==crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MbisP and a synthetic peptide containing the NR2 box of DRIP 205==		==crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MbisP and a synthetic peptide containing the NR2 box of DRIP 205==
	<StructureSection load='1rkg' size='340' side='right' caption='[[1rkg]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1rkg' size='340' side='right' caption='[[1rkg]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rjk\|1rjk]], [[1rk3\|1rk3]], [[1rkh\|1rkh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rjk\|1rjk]], [[1rk3\|1rk3]], [[1rkh\|1rkh]]</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 ([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=1rkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkg OCA], [http://pdbe.org/1rkg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rkg RCSB], [http://www.ebi.ac.uk/pdbsum/1rkg 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=1rkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkg OCA], [http://pdbe.org/1rkg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rkg RCSB], [http://www.ebi.ac.uk/pdbsum/1rkg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rkg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1rkg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1rkg" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Sandbox vdr\|Sandbox vdr]]
-	*[[Vitamin D receptor\|Vitamin D receptor]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:43, 9 February 2016

OCA — Tue, 09 Feb 2016 15:43:37 GMT

←Older revision		Revision as of 15:43, 9 February 2016
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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=1rkg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:41, 10 September 2015

OCA — Thu, 10 Sep 2015 23:41:33 GMT

←Older revision		Revision as of 23:41, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1rkg' size='340' side='right' caption='[[1rkg]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1rkg' size='340' side='right' caption='[[1rkg]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rkg]] 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=1RKG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RKG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rkg]] 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=1RKG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RKG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=VD1:5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIOL'>VD1</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=VD1:5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIOL'>VD1</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rjk\|1rjk]], [[1rk3\|1rk3]], [[1rkh\|1rkh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rjk\|1rjk]], [[1rk3\|1rk3]], [[1rkh\|1rkh]]</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=1rkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rkg RCSB], [http://www.ebi.ac.uk/pdbsum/1rkg 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=1rkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkg OCA], [http://pdbe.org/1rkg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rkg RCSB], [http://www.ebi.ac.uk/pdbsum/1rkg PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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 1rkg" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rattus norvegicus~~]]	+	[[Category: Buffalo rat]]
	[[Category: Bauer, C B]]		[[Category: Bauer, C B]]
	[[Category: Benning, M M]]		[[Category: Benning, M M]]

OCA at 07:49, 25 December 2014

OCA — Thu, 25 Dec 2014 07:49:52 GMT

←Older revision		Revision as of 07:49, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rkg]] 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=1RKG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RKG FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rkg]] 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=1RKG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RKG FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=VD1:5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIOL'>VD1</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=VD1:5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIOL'>VD1</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rjk\|1rjk]], [[1rk3\|1rk3]], [[1rkh\|1rkh]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rjk\|1rjk]], [[1rk3\|1rk3]], [[1rkh\|1rkh]]</td></tr>
-	<tr><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 Rattus norvegicus])</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=1rkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rkg RCSB], [http://www.ebi.ac.uk/pdbsum/1rkg 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=1rkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rkg RCSB], [http://www.ebi.ac.uk/pdbsum/1rkg 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 35:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: Bauer, C B.]]	+	[[Category: Bauer, C B]]
-	[[Category: Benning, M M.]]	+	[[Category: Benning, M M]]
-	[[Category: DeLuca, H F.]]	+	[[Category: DeLuca, H F]]
-	[[Category: Pike, J W.]]	+	[[Category: Pike, J W]]
-	[[Category: Vanhooke, J L.]]	+	[[Category: Vanhooke, J L]]
	[[Category: Hormone-growth factor receptor complex]]		[[Category: Hormone-growth factor receptor complex]]
	[[Category: Nuclear receptor-coactivator interaction]]		[[Category: Nuclear receptor-coactivator interaction]]
	[[Category: Nuclear receptor-ligand complex]]		[[Category: Nuclear receptor-ligand complex]]

OCA at 20:34, 28 September 2014

OCA — Sun, 28 Sep 2014 20:34:49 GMT

←Older revision		Revision as of 20:34, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1rkg.~~png~~\|~~left~~\|200px]]	+	==crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MbisP and a synthetic peptide containing the NR2 box of DRIP 205==
		+	<StructureSection load='1rkg' size='340' side='right' caption='[[1rkg]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1rkg]] 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=1RKG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RKG FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=VD1:5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIOL'>VD1</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rjk\|1rjk]], [[1rk3\|1rk3]], [[1rkh\|1rkh]]</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rkg RCSB], [http://www.ebi.ac.uk/pdbsum/1rkg 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/rk/1rkg_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 ==
		+	We have determined the crystal structures of the ligand binding domain (LBD) of the rat vitamin D receptor in ternary complexes with a synthetic LXXLL-containing peptide and the following four ligands: 1alpha,25-dihydroxyvitamin D(3); 2-methylene-19-nor-(20S)-1alpha,25-dihydroxyvitamin D(3) (2MD); 1alpha-hydroxy-2-methylene-19-nor-(20S)-bishomopregnacalciferol (2MbisP), and 2alpha-methyl-19-nor-1alpha,25-dihydroxyvitamin D(3) (2AM20R). The conformation of the LBD is identical in each complex. Binding of the 2-carbon-modified analogues does not change the positions of the amino acids in the ligand binding site and has no effect on the interactions in the coactivator binding pocket. The CD ring of the superpotent analogue, 2MD, is tilted within the binding site relative to the other ligands in this study and to (20S)-1alpha,25-dihydroxyvitamin D(3) [Tocchini-Valentini et al. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 5491-5496]. The aliphatic side chain of 2MD follows a different path within the binding site; nevertheless, the 25-hydroxyl group at the end of the chain occupies the same position as that of the natural ligand, and the hydrogen bonds with histidines 301 and 393 are maintained. 2MbisP binds to the receptor despite the absence of the 25-hydroxyl group. A water molecule is observed between His 301 and His 393 in this structure, and it preserves the orientation of the histidines in the binding site. Although the alpha-chair conformer is highly favored in solution for the A ring of 2AM20R, the crystal structures demonstrate that this ring assumes the beta-chair conformation in all cases, and the 1alpha-hydroxyl group is equatorial. The peptide folds as a helix and is anchored through hydrogen bonds to a surface groove formed by helices 3, 4, and 12. Electrostatic and hydrophobic interactions between the peptide and the LBD stabilize the active receptor conformation. This stablization appears necessary for crystal growth.

-	~~{{STRUCTURE_1rkg\| PDB=1rkg \| SCENE= }}~~	+	Molecular structure of the rat vitamin D receptor ligand binding domain complexed with 2-carbon-substituted vitamin D3 hormone analogues and a LXXLL-containing coactivator peptide.,Vanhooke JL, Benning MM, Bauer CB, Pike JW, DeLuca HF Biochemistry. 2004 Apr 13;43(14):4101-10. PMID:15065852<ref>PMID:15065852</ref>

-	~~===crystal structure~~ of the ~~rat vitamin D receptor ligand binding domain complexed with 2MbisP 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_15065852}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1rkg]] 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=1RKG OCA].~~	+

	==See Also==		==See Also==
		+	*[[Sandbox vdr\|Sandbox vdr]]
	*[[Vitamin D receptor\|Vitamin D receptor]]		*[[Vitamin D receptor\|Vitamin D receptor]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015065852<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Bauer, C B.]]		[[Category: Bauer, C B.]]

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

OCA — Sat, 20 Oct 2012 14:20:33 GMT

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

←Older revision

Revision as of 14:20, 20 October 2012

OCA at 14:20, 20 October 2012

OCA — Sat, 20 Oct 2012 14:20:31 GMT

←Older revision		Revision as of 14:20, 20 October 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1rkg.png\|left\|200px]]		[[Image:1rkg.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1rkg", 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_1rkg\| PDB=1rkg \| SCENE= }}		{{STRUCTURE_1rkg\| PDB=1rkg \| SCENE= }}

	===crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MbisP and a synthetic peptide containing the NR2 box of DRIP 205===		===crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MbisP and a synthetic peptide containing the NR2 box of DRIP 205===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15065852}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15065852 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15065852}}		{{ABSTRACT_PUBMED_15065852}}

	==About this Structure==		==About this Structure==
-	~~1RKG~~ is a 2 ~~chains~~ structure ~~of 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=1RKG OCA].	+	[[1rkg]] 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=1RKG OCA].
		+
		+	==See Also==
		+	*[[Vitamin D receptor\|Vitamin D receptor]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15065852~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015065852</ref><references group="xtra"/>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Bauer, C B.]]		[[Category: Bauer, C B.]]
Line 30:		Line 21:
	[[Category: Pike, J W.]]		[[Category: Pike, J W.]]
	[[Category: Vanhooke, J L.]]		[[Category: Vanhooke, J L.]]
		+	[[Category: Hormone-growth factor receptor complex]]
	[[Category: Nuclear receptor-coactivator interaction]]		[[Category: Nuclear receptor-coactivator interaction]]
	[[Category: Nuclear receptor-ligand complex]]		[[Category: Nuclear receptor-ligand complex]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:55:12 2009''

OCA at 08:55, 17 February 2009

OCA — Tue, 17 Feb 2009 08:55:13 GMT

←Older revision		Revision as of 08:55, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1RKG is a ~~[[Protein complex]]~~ structure of 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=1RKG OCA].	+	1RKG is a 2 chains structure of 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=1RKG OCA].

	==Reference==		==Reference==
-	Molecular structure of the rat vitamin D receptor ligand binding domain complexed with 2-carbon-substituted vitamin D3 hormone analogues and a LXXLL-containing coactivator peptide., Vanhooke JL, Benning MM, Bauer CB, Pike JW, DeLuca HF, Biochemistry. 2004 Apr 13;43(14):4101-10. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15065852 15065852]~~	+	<ref group="xtra">PMID:15065852</ref><references group="xtra"/>
-	~~[[Category: Protein complex]]~~	+
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Bauer, C B.]]		[[Category: Bauer, C B.]]
Line 34:		Line 33:
	[[Category: Nuclear receptor-ligand complex]]		[[Category: Nuclear receptor-ligand complex]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 14~~:54:~~18 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:55:12 2009''