3w5q - Revision history

OCA at 08:44, 20 March 2024

OCA — Wed, 20 Mar 2024 08:44:05 GMT

←Older revision		Revision as of 08:44, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='3w5q' size='340' side='right'caption='[[3w5q]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3w5q' size='340' side='right'caption='[[3w5q]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3w5q]] 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=3W5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W5Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3w5q]] 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=3W5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W5Q FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=3KL:(5BETA~~,~~9BETA)-3-OXOCHOLAN-24-OIC+ACID'>3KL</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;~~'>~~[[3w5p\|3w5p]], [[3w5r\|3w5r]], [[3w5t\|3w5t]]~~</~~div~~>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3KL:(5BETA,9BETA)-3-OXOCHOLAN-24-OIC+ACID'>3KL</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=3w5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w5q OCA], [https://pdbe.org/3w5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w5q RCSB], [https://www.ebi.ac.uk/pdbsum/3w5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w5q 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=3w5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w5q OCA], [https://pdbe.org/3w5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w5q RCSB], [https://www.ebi.ac.uk/pdbsum/3w5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w5q 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>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The secondary bile acid lithocholic acid (LCA) and its derivatives act as selective modulators of the vitamin D receptor (VDR), although their structures fundamentally differ from that of the natural hormone 1alpha,25-dihydroxyvitamin D3 (1,25(OH)2D3). Here, we have determined the crystal structures of the ligand binding domain of rat VDR (VDR-LBD) in ternary complexes with a synthetic partial peptide of the coactivator MED1 (Mediator of RNA polymerase II transcription subunit 1) and four ligands, LCA, 3-keto LCA, LCA acetate, and LCA propionate, with the goal of elucidating their agonistic mechanism. LCA and its derivatives bind to the same ligand-binding pocket (LBP) of VDR-LBD that 1,25(OH)2D3 binds to, but in the opposite orientation; their A-ring is positioned at the top of the LBP, whereas their acyclic tail is located at the bottom of the LBP. However, most of the hydrophobic and hydrophilic interactions observed in the complex with 1,25(OH)2D3 are reproduced in the complexes with LCA and its derivatives. Additional interactions between VDR-LBD and the C-3 substituents of the A-ring are also observed in the complexes with LCA and its derivatives. These may result in the observed difference in the potency among the LCA-type ligands.	+
-		+
-	Crystal structures of complexes of vitamin D receptor ligand-binding domain with lithocholic acid derivatives.,Masuno H, Ikura T, Morizono D, Orita I, Yamada S, Shimizu M, Ito N J Lipid Res. 2013 May 30. PMID:23723390<ref>PMID:23723390</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3w5q" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 28:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Buffalo rat~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ikura, T~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: ~~Ito, N~~]]	+	[[Category: Ikura T]]
-	[[Category: ~~Masuno, H~~]]	+	[[Category: Ito N]]
-	[[Category: ~~Activator]]~~	+	[[Category: Masuno H]]
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Nuclear receptor-agonist complex]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Receptor]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Zinc-finger~~]]	+

OCA at 05:23, 3 August 2022

OCA — Wed, 03 Aug 2022 05:23:24 GMT

←Older revision		Revision as of 05:23, 3 August 2022
Line 1:		Line 1:

	==Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives==		==Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives==
-	<StructureSection load='3w5q' size='340' side='right' caption='[[3w5q]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='3w5q' size='340' side='right'caption='[[3w5q]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3w5q]] 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=3W5Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3W5Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3w5q]] 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=3W5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W5Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3KL:(5BETA,9BETA)-3-OXOCHOLAN-24-OIC+ACID'>3KL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3KL:(5BETA,9BETA)-3-OXOCHOLAN-24-OIC+ACID'>3KL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3w5p\|3w5p]], [[3w5r\|3w5r]], [[3w5t\|3w5t]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3w5p\|3w5p]], [[3w5r\|3w5r]], [[3w5t\|3w5t]]</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=3w5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w5q OCA], [~~http~~://pdbe.org/3w5q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3w5q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3w5q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3w5q 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=3w5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w5q OCA], [https://pdbe.org/3w5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w5q RCSB], [https://www.ebi.ac.uk/pdbsum/3w5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w5q 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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 3w5q" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3w5q" 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 25:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
		+	[[Category: Large Structures]]
	[[Category: Ikura, T]]		[[Category: Ikura, T]]
	[[Category: Ito, N]]		[[Category: Ito, N]]

OCA at 08:00, 22 November 2017

OCA — Wed, 22 Nov 2017 08:00:36 GMT

←Older revision		Revision as of 08:00, 22 November 2017
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 3w5q" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3w5q" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Sandbox vdr\|Sandbox vdr]]
-	*[[Vitamin D receptor\|Vitamin D receptor]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:48, 5 August 2016

OCA — Fri, 05 Aug 2016 20:48:47 GMT

←Older revision		Revision as of 20:48, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives==		==Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives==
	<StructureSection load='3w5q' size='340' side='right' caption='[[3w5q]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3w5q' size='340' side='right' caption='[[3w5q]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3w5p\|3w5p]], [[3w5r\|3w5r]], [[3w5t\|3w5t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3w5p\|3w5p]], [[3w5r\|3w5r]], [[3w5t\|3w5t]]</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=3w5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w5q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w5q RCSB], [http://www.ebi.ac.uk/pdbsum/3w5q 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=3w5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w5q OCA], [http://pdbe.org/3w5q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3w5q RCSB], [http://www.ebi.ac.uk/pdbsum/3w5q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3w5q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 3w5q" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 21:47, 25 December 2014

OCA — Thu, 25 Dec 2014 21:47:45 GMT

←Older revision		Revision as of 21:47, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3w5q\| PDB=3w5q \| SCENE= }}~~	+	==Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives==
-	===Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives===	+	<StructureSection load='3w5q' size='340' side='right' caption='[[3w5q]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23723390}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[3w5q]] 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=3W5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W5Q FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3KL:(5BETA,9BETA)-3-OXOCHOLAN-24-OIC+ACID'>3KL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3w5p\|3w5p]], [[3w5r\|3w5r]], [[3w5t\|3w5t]]</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=3w5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w5q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w5q RCSB], [http://www.ebi.ac.uk/pdbsum/3w5q PDBsum]</span></td></tr>
		+	</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>		[[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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The secondary bile acid lithocholic acid (LCA) and its derivatives act as selective modulators of the vitamin D receptor (VDR), although their structures fundamentally differ from that of the natural hormone 1alpha,25-dihydroxyvitamin D3 (1,25(OH)2D3). Here, we have determined the crystal structures of the ligand binding domain of rat VDR (VDR-LBD) in ternary complexes with a synthetic partial peptide of the coactivator MED1 (Mediator of RNA polymerase II transcription subunit 1) and four ligands, LCA, 3-keto LCA, LCA acetate, and LCA propionate, with the goal of elucidating their agonistic mechanism. LCA and its derivatives bind to the same ligand-binding pocket (LBP) of VDR-LBD that 1,25(OH)2D3 binds to, but in the opposite orientation; their A-ring is positioned at the top of the LBP, whereas their acyclic tail is located at the bottom of the LBP. However, most of the hydrophobic and hydrophilic interactions observed in the complex with 1,25(OH)2D3 are reproduced in the complexes with LCA and its derivatives. Additional interactions between VDR-LBD and the C-3 substituents of the A-ring are also observed in the complexes with LCA and its derivatives. These may result in the observed difference in the potency among the LCA-type ligands.

-	~~==About this Structure==~~	+	Crystal structures of complexes of vitamin D receptor ligand-binding domain with lithocholic acid derivatives.,Masuno H, Ikura T, Morizono D, Orita I, Yamada S, Shimizu M, Ito N J Lipid Res. 2013 May 30. PMID:23723390<ref>PMID:23723390</ref>
-	~~[[3w5q]] 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=3W5Q OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Sandbox vdr\|Sandbox vdr]]		*[[Sandbox vdr\|Sandbox vdr]]
	*[[Vitamin D receptor\|Vitamin D receptor]]		*[[Vitamin D receptor\|Vitamin D receptor]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:023723390</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
-	[[Category: Ikura, T.]]	+	[[Category: Ikura, T]]
-	[[Category: Ito, N.]]	+	[[Category: Ito, N]]
-	[[Category: Masuno, H.]]	+	[[Category: Masuno, H]]
	[[Category: Activator]]		[[Category: Activator]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]

OCA at 06:03, 29 January 2014

OCA — Wed, 29 Jan 2014 06:03:42 GMT

←Older revision		Revision as of 06:03, 29 January 2014
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
-	[[3w5q]] 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=3W5Q OCA].	+	[[3w5q]] 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=3W5Q OCA].
		+
		+	==See Also==
		+	*[[Sandbox vdr\|Sandbox vdr]]
		+	*[[Vitamin D receptor\|Vitamin D receptor]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:023723390</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:023723390</ref><references group="xtra"/><references/>
-	[[Category: ~~Rattus norvegicus~~]]	+	[[Category: Buffalo rat]]
	[[Category: Ikura, T.]]		[[Category: Ikura, T.]]
	[[Category: Ito, N.]]		[[Category: Ito, N.]]

OCA at 10:12, 30 June 2013

OCA — Sun, 30 Jun 2013 10:12:56 GMT

←Older revision		Revision as of 10:12, 30 June 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_3w5q\| PDB=3w5q \| SCENE= }}
		+	===Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives===
		+	{{ABSTRACT_PUBMED_23723390}}

-	~~The entry 3w5q~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	==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>

-	~~Authors~~: ~~Masuno, H~~.~~, Ikura, T~~.~~, Ito, N~~.	+	==About this Structure==
		+	[[3w5q]] 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=3W5Q OCA].

-	~~Description~~: ~~Crystal structure of complexes of vitamin D receptor ligand~~ binding ~~domain with lithocholic acid derivatives~~	+	==Reference==
		+	<ref group="xtra">PMID:023723390</ref><references group="xtra"/><references/>
		+	[[Category: Rattus norvegicus]]
		+	[[Category: Ikura, T.]]
		+	[[Category: Ito, N.]]
		+	[[Category: Masuno, H.]]
		+	[[Category: Activator]]
		+	[[Category: Dna-binding]]
		+	[[Category: Metal-binding]]
		+	[[Category: Nuclear receptor-agonist complex]]
		+	[[Category: Nucleus]]
		+	[[Category: Phosphoprotein]]
		+	[[Category: Receptor]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription regulation]]
		+	[[Category: Zinc-finger]]

OCA at 14:04, 27 February 2013

OCA — Wed, 27 Feb 2013 14:04:38 GMT

←Older revision		Revision as of 14:04, 27 February 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3w5q is ON HOLD	+	The entry 3w5q is ON HOLD until Paper Publication

	Authors: Masuno, H., Ikura, T., Ito, N.		Authors: Masuno, H., Ikura, T., Ito, N.

	Description: Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives		Description: Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives

OCA: Protected "3w5q" [edit=sysop:move=sysop]

OCA — Wed, 13 Feb 2013 09:51:30 GMT

Protected "3w5q" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:51, 13 February 2013

OCA: New page: '''Unreleased structure''' The entry 3w5q is ON HOLD Authors: Masuno, H., Ikura, T., Ito, N. Description: Crystal structure of complexes of vitamin D receptor ligand binding domain wit...

OCA — Wed, 13 Feb 2013 09:51:29 GMT

New page: '''Unreleased structure''' The entry 3w5q is ON HOLD Authors: Masuno, H., Ikura, T., Ito, N. Description: Crystal structure of complexes of vitamin D receptor ligand binding domain wit...

New page

'''Unreleased structure'''

The entry 3w5q is ON HOLD

Authors: Masuno, H., Ikura, T., Ito, N.

Description: Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives