3vrt - Revision history

OCA at 08:41, 20 March 2024

2024-03-20T08:41:32Z

← Older revision		Revision as of 08:41, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='3vrt' size='340' side='right'caption='[[3vrt]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3vrt' size='340' side='right'caption='[[3vrt]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3vrt]] 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=3VRT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VRT FirstGlance]. <br>		<table><tr><td colspan='2'>[[3vrt]] 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=3VRT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VRT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=YS2:(1R,3R,7E,17BETA)-17-[(2R)-5-HYDROXYPENTAN-2-YL]-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>YS2</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]] 2.4Å</td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3vru\|3vru]], [[3vrv\|3vrv]], [[3vrw\|3vrw]]</div></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=YS2:(1R,3R,7E,17BETA)-17-[(2R)-5-HYDROXYPENTAN-2-YL]-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>YS2</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=3vrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrt OCA], [https://pdbe.org/3vrt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vrt RCSB], [https://www.ebi.ac.uk/pdbsum/3vrt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vrt 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=3vrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrt OCA], [https://pdbe.org/3vrt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vrt RCSB], [https://www.ebi.ac.uk/pdbsum/3vrt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vrt 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 ==~~
	Previously, we reported that 22S-butyl-25,26,27-trinor-1alpha,24-dihydroxyvitamin D(3)2 represents a new class of antagonist for the vitamin D receptor (VDR). The crystal structure of the ligand-binding domain (LBD) of VDR complexed with 2 showed the formation of a butyl pocket to accommodate the 22-butyl group and insufficient interactions between ligand 2 and the C-terminus of VDR. Here, we designed and synthesized new analogues 5a-c and evaluated their biological activities to probe whether agonistic activity is recovered when the analogue restores interactions with the C-terminus of VDR. Analogues 5a-c exhibited full agonistic activity in transactivation. Interestingly, 5c, which bears a 24-diethyl group, completely recovered agonistic activity, although 3c and 4c act as an antagonist and a weak agonist, respectively. The crystal structures of VDR-LBD complexed with 3a, 4a, 5a, and 5c were solved, and the results confirmed that butyl pocket formation in VDR strongly affects the agonistic or antagonistic behaviors of ligands.

	Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands.,Yoshimoto N, Sakamaki Y, Haeta M, Kato A, Inaba Y, Itoh T, Nakabayashi M, Ito N, Yamamoto K J Med Chem. 2012 May 10;55(9):4373-81. Epub 2012 Apr 27. PMID:22512505<ref>PMID:22512505</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 3vrt" 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: Inaba, Y]]		[[Category: Rattus norvegicus]]
	[[Category: Ito, N]]		[[Category: Inaba Y]]
	[[Category: Itoh, T]]		[[Category: Ito N]]
	[[Category: Nakabayashi, M]]		[[Category: Itoh T]]
	[[Category: Yamamoto, K]]		[[Category: Nakabayashi M]]
	[[Category: Yoshimoto, N]]		[[Category: Yamamoto K]]
	~~[[Category: Co-factor]]~~		[[Category: Yoshimoto N]]
	~~[[Category: Nuclear]]~~
	~~[[Category: Rxr]]~~
	~~[[Category: Transcription]]~~
	~~[[Category: Vdre]]~~
	~~[[Category: Vitamin d3~~]]

OCA at 19:00, 27 July 2022

2022-07-27T19:00:44Z

← Older revision		Revision as of 19:00, 27 July 2022
Line 1:		Line 1:

	==VDR ligand binding domain in complex with 2-Mehylidene-19,25,26,27-tetranor-1alpha,24-dihydroxyvitaminD3==		==VDR ligand binding domain in complex with 2-Mehylidene-19,25,26,27-tetranor-1alpha,24-dihydroxyvitaminD3==
	<StructureSection load='3vrt' size='340' side='right' caption='[[3vrt]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3vrt' size='340' side='right'caption='[[3vrt]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3vrt]] 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=3VRT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3VRT FirstGlance]. <br>		<table><tr><td colspan='2'>[[3vrt]] 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=3VRT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VRT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YS2:(1R,3R,7E,17BETA)-17-[(2R)-5-HYDROXYPENTAN-2-YL]-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>YS2</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=YS2:(1R,3R,7E,17BETA)-17-[(2R)-5-HYDROXYPENTAN-2-YL]-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>YS2</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vru\|3vru]], [[3vrv\|3vrv]], [[3vrw\|3vrw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3vru\|3vru]], [[3vrv\|3vrv]], [[3vrw\|3vrw]]</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=3vrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrt OCA], [~~http~~://pdbe.org/3vrt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3vrt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3vrt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3vrt 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=3vrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrt OCA], [https://pdbe.org/3vrt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vrt RCSB], [https://www.ebi.ac.uk/pdbsum/3vrt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vrt 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 ==
Line 23:		Line 23:
	==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 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
			[[Category: Large Structures]]
	[[Category: Inaba, Y]]		[[Category: Inaba, Y]]
	[[Category: Ito, N]]		[[Category: Ito, N]]

OCA at 00:53, 5 August 2016

2016-08-05T00:53:11Z

← Older revision		Revision as of 00:53, 5 August 2016
Line 1:		Line 1:

	==VDR ligand binding domain in complex with 2-Mehylidene-19,25,26,27-tetranor-1alpha,24-dihydroxyvitaminD3==		==VDR ligand binding domain in complex with 2-Mehylidene-19,25,26,27-tetranor-1alpha,24-dihydroxyvitaminD3==
	<StructureSection load='3vrt' size='340' side='right' caption='[[3vrt]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3vrt' size='340' side='right' caption='[[3vrt]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3vrt]] 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=3VRT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VRT FirstGlance]. <br>		<table><tr><td colspan='2'>[[3vrt]] 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=3VRT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VRT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YS2:(1R,3R,7E,17BETA)-17-[(2R)-5-HYDROXYPENTAN-2-YL]-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>YS2</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YS2:(1R,3R,7E,17BETA)-17-[(2R)-5-HYDROXYPENTAN-2-YL]-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>YS2</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vru\|3vru]], [[3vrv\|3vrv]], [[3vrw\|3vrw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vru\|3vru]], [[3vrv\|3vrv]], [[3vrw\|3vrw]]</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=3vrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vrt RCSB], [http://www.ebi.ac.uk/pdbsum/3vrt 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=3vrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrt OCA], [http://pdbe.org/3vrt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vrt RCSB], [http://www.ebi.ac.uk/pdbsum/3vrt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vrt 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 3vrt" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Rattus norvegicus~~]]		[[Category: Buffalo rat]]
	[[Category: Inaba, Y]]		[[Category: Inaba, Y]]
	[[Category: Ito, N]]		[[Category: Ito, N]]

OCA at 14:30, 25 December 2014

2014-12-25T14:30:58Z

← Older revision		Revision as of 14:30, 25 December 2014
Line 1:		Line 1:
	[[~~Image~~:~~3vrt~~.~~jpg~~\|~~left~~\|~~200px~~]]		==VDR ligand binding domain in complex with 2-Mehylidene-19,25,26,27-tetranor-1alpha,24-dihydroxyvitaminD3==
			<StructureSection load='3vrt' size='340' side='right' caption='[[3vrt]], [[Resolution\|resolution]] 2.40Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3vrt]] 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=3VRT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VRT FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YS2:(1R,3R,7E,17BETA)-17-[(2R)-5-HYDROXYPENTAN-2-YL]-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>YS2</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vru\|3vru]], [[3vrv\|3vrv]], [[3vrw\|3vrw]]</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=3vrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vrt RCSB], [http://www.ebi.ac.uk/pdbsum/3vrt 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>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Previously, we reported that 22S-butyl-25,26,27-trinor-1alpha,24-dihydroxyvitamin D(3)2 represents a new class of antagonist for the vitamin D receptor (VDR). The crystal structure of the ligand-binding domain (LBD) of VDR complexed with 2 showed the formation of a butyl pocket to accommodate the 22-butyl group and insufficient interactions between ligand 2 and the C-terminus of VDR. Here, we designed and synthesized new analogues 5a-c and evaluated their biological activities to probe whether agonistic activity is recovered when the analogue restores interactions with the C-terminus of VDR. Analogues 5a-c exhibited full agonistic activity in transactivation. Interestingly, 5c, which bears a 24-diethyl group, completely recovered agonistic activity, although 3c and 4c act as an antagonist and a weak agonist, respectively. The crystal structures of VDR-LBD complexed with 3a, 4a, 5a, and 5c were solved, and the results confirmed that butyl pocket formation in VDR strongly affects the agonistic or antagonistic behaviors of ligands.

	~~<!--~~		Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands.,Yoshimoto N, Sakamaki Y, Haeta M, Kato A, Inaba Y, Itoh T, Nakabayashi M, Ito N, Yamamoto K J Med Chem. 2012 May 10;55(9):4373-81. Epub 2012 Apr 27. PMID:22512505<ref>PMID:22512505</ref>
	~~The line below this paragraph~~, ~~containing "STRUCTURE_3vrt"~~, ~~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_3vrt\| PDB=3vrt \| SCENE= }}~~

	~~===VDR ligand binding domain in complex with 2-Mehylidene-19~~,~~25,26,27-tetranor-1alpha,24-dihydroxyvitaminD3===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>

			==See Also==
	~~<!--~~		*[[Sandbox vdr\|Sandbox vdr]]
	~~The line below this paragraph, {{ABSTRACT_PUBMED_22512505}}, adds the Publication Abstract to the page~~		*[[Vitamin D receptor\|Vitamin D receptor]]
	~~(as it appears on PubMed at http://www.pubmed.gov), where 22512505 is the PubMed ID number.~~		== References ==
	~~-->~~		<references/>
	~~{{ABSTRACT_PUBMED_22512505}}~~		__TOC__
			</StructureSection>
	==~~About this Structure~~==
	[[~~3vrt~~]] ~~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=3VRT OCA~~].

	==~~Reference~~==
	<~~ref group="xtra">PMID:022512505<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Inaba, Y.]]		[[Category: Inaba, Y]]
	[[Category: Ito, N.]]		[[Category: Ito, N]]
	[[Category: Itoh, T.]]		[[Category: Itoh, T]]
	[[Category: Nakabayashi, M.]]		[[Category: Nakabayashi, M]]
	[[Category: Yamamoto, K.]]		[[Category: Yamamoto, K]]
	[[Category: Yoshimoto, N.]]		[[Category: Yoshimoto, N]]
	[[Category: Co-factor]]		[[Category: Co-factor]]
	[[Category: Nuclear]]		[[Category: Nuclear]]

OCA at 06:01, 23 May 2012

2012-05-23T06:01:39Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+[[Image:3vrt.jpg|left|200px]]
-The entry 3vrt is ON HOLD
+<!--
-Authors: Nakabayashi, M., Yoshimoto, N., Inaba, Y., Itoh, T., Ito, N., Yamamoto, K.
+===VDR ligand binding domain in complex with 2-Mehylidene-19,25,26,27-tetranor-1alpha,24-dihydroxyvitaminD3===
-Description: VDR ligand binding domain in complex with 2-Mehylidene-19,25,26,27-tetranor-1alpha,24-dihydroxyvitaminD3

OCA at 18:46, 2 May 2012

2012-05-02T18:46:35Z

← Older revision		Revision as of 18:46, 2 May 2012
Line 5:		Line 5:
	Authors: Nakabayashi, M., Yoshimoto, N., Inaba, Y., Itoh, T., Ito, N., Yamamoto, K.		Authors: Nakabayashi, M., Yoshimoto, N., Inaba, Y., Itoh, T., Ito, N., Yamamoto, K.

	Description: VDR ligand binding domain in complex with 2-Mehylidene-19,25,26,27-tetranor-~~1α~~,24-dihydroxyvitaminD3		Description: VDR ligand binding domain in complex with 2-Mehylidene-19,25,26,27-tetranor-1alpha,24-dihydroxyvitaminD3

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

2012-04-25T08:40:21Z

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

← Older revision	Revision as of 08:40, 25 April 2012
(No difference)

OCA: New page: '''Unreleased structure''' The entry 3vrt is ON HOLD Authors: Nakabayashi, M., Yoshimoto, N., Inaba, Y., Itoh, T., Ito, N., Yamamoto, K. Description: VDR ligand binding domain in compl...

2012-04-25T08:40:20Z

New page: '''Unreleased structure''' The entry 3vrt is ON HOLD Authors: Nakabayashi, M., Yoshimoto, N., Inaba, Y., Itoh, T., Ito, N., Yamamoto, K. Description: VDR ligand binding domain in compl...

New page

'''Unreleased structure'''

The entry 3vrt is ON HOLD

Authors: Nakabayashi, M., Yoshimoto, N., Inaba, Y., Itoh, T., Ito, N., Yamamoto, K.

Description: VDR ligand binding domain in complex with 2-Mehylidene-19,25,26,27-tetranor-1α,24-dihydroxyvitaminD3