2zmj - Revision history

OCA at 13:57, 13 March 2024

OCA — Wed, 13 Mar 2024 13:57:55 GMT

←Older revision		Revision as of 13:57, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='2zmj' size='340' side='right'caption='[[2zmj]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='2zmj' size='340' side='right'caption='[[2zmj]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zmj]] 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=2ZMJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZMJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zmj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] and [https://en.wikipedia.org/wiki/Xenopus_tropicalis Xenopus tropicalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZMJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZMJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MI4:(1R,3R,7E,17BETA)-17-{(1S,2E,5R)-5-HYDROXY-1-METHYL-6-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]HEX-2-EN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>MI4</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]] 2.35Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2zmh\|2zmh]], [[2zmi\|2zmi]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MI4:(1R,3R,7E,17BETA)-17-{(1S,2E,5R)-5-HYDROXY-1-METHYL-6-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]HEX-2-EN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>MI4</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=2zmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zmj OCA], [https://pdbe.org/2zmj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zmj RCSB], [https://www.ebi.ac.uk/pdbsum/2zmj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zmj 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=2zmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zmj OCA], [https://pdbe.org/2zmj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zmj RCSB], [https://www.ebi.ac.uk/pdbsum/2zmj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zmj 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_XENTR MED1_XENTR]] 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 (By similarity).	+	[https://www.uniprot.org/uniprot/VDR_RAT VDR_RAT] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:17227670</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</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=2zmj 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=2zmj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The X-ray crystal structures of the rat VDR ligand-binding domain complexed with 19-norvitamin D compounds that contain an adamantyl substituent at the side-chain terminus, 2a (ADTT), 2b (ADNY), and 2c (ADMI4) and a coactivator peptide derived from DRIP205 are reported. These compounds show a series of partial agonistic (10-75% efficacy)/antagonistic activities. All of these complexed receptors are crystallized in the canonical active conformation, regardless of their activity profiles. The bulky adamantyl side chain does not crowd helix 12 but protrudes into the gap formed by helix 11, loop 11-12, helix 3, and loop 6-7, thereby widening the ligand binding pocket. We suggest that these structural changes destabilize the active protein conformation and reduce its contribution to equilibrium among the active and inactive conformations. The coactivator peptide traps the minor active conformation, and the equilibrium shifts to the active conformation. As a result, these ligands show partial agonistic activities.
-
-	Crystal Structures of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and Partial Agonism.,Nakabayashi M, Yamada S, Yoshimoto N, Tanaka T, Igarashi M, Ikura T, Ito N, Makishima M, Tokiwa H, Deluca HF, Shimizu M J Med Chem. 2008 Aug 19. PMID:18710208<ref>PMID:18710208</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2zmj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 38:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Buffalo rat]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: DeLuca~~, H F~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: Igarashi, M]]	+	[[Category: Xenopus tropicalis]]
-	[[Category: Ikura, T]]	+	[[Category: DeLuca HF]]
-	[[Category: Ito, N]]	+	[[Category: Igarashi M]]
-	[[Category: Makishima, M]]	+	[[Category: Ikura T]]
-	[[Category: Nakabayashi, M]]	+	[[Category: Ito N]]
-	[[Category: Shimizu, M]]	+	[[Category: Makishima M]]
-	[[Category: Tanaka, T]]	+	[[Category: Nakabayashi M]]
-	[[Category: Tokiwa, H]]	+	[[Category: Shimizu M]]
-	[[Category: Yamada, S]]	+	[[Category: Tanaka T]]
-	[[Category: Yoshimoto, N]]	+	[[Category: Tokiwa H]]
-	~~[[Category: Activator]]~~	+	[[Category: Yamada S]]
-	~~[[Category: Dna-binding]]~~	+	[[Category: Yoshimoto N]]
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Nuclear receptor-antagonist complex]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Receptor]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Zinc]]~~	+
-	~~[[Category: Zinc-finger~~]]	+

OCA at 17:32, 15 December 2021

OCA — Wed, 15 Dec 2021 17:32:58 GMT

←Older revision		Revision as of 17:32, 15 December 2021
Line 1:		Line 1:

	==Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism==		==Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism==
-	<StructureSection load='2zmj' size='340' side='right' caption='[[2zmj]], [[Resolution\|resolution]] 2.35Å' scene=''>	+	<StructureSection load='2zmj' size='340' side='right'caption='[[2zmj]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zmj]] 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=2ZMJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2ZMJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zmj]] 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=2ZMJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZMJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MI4:(1R,3R,7E,17BETA)-17-{(1S,2E,5R)-5-HYDROXY-1-METHYL-6-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]HEX-2-EN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>MI4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MI4:(1R,3R,7E,17BETA)-17-{(1S,2E,5R)-5-HYDROXY-1-METHYL-6-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]HEX-2-EN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>MI4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zmh\|2zmh]], [[2zmi\|2zmi]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2zmh\|2zmh]], [[2zmi\|2zmi]]</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=2zmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zmj OCA], [~~http~~://pdbe.org/2zmj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2zmj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2zmj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2zmj 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=2zmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zmj OCA], [https://pdbe.org/2zmj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zmj RCSB], [https://www.ebi.ac.uk/pdbsum/2zmj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zmj 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_XENTR MED1_XENTR]] 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 (By similarity).	+	[[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_XENTR MED1_XENTR]] 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 (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
	*[[Sandbox vdr\|Sandbox vdr]]		*[[Sandbox vdr\|Sandbox vdr]]
-	*[[Vitamin D receptor\|Vitamin D receptor]]	+	*[[Vitamin D receptor 3D structures\|Vitamin D receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
		+	[[Category: Large Structures]]
	[[Category: DeLuca, H F]]		[[Category: DeLuca, H F]]
	[[Category: Igarashi, M]]		[[Category: Igarashi, M]]

OCA at 07:31, 18 October 2018

OCA — Thu, 18 Oct 2018 07:31:26 GMT

←Older revision		Revision as of 07:31, 18 October 2018
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/zm/2zmj_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zm/2zmj_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 59:		Line 59:
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
		+	[[Category: Zinc]]
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

OCA at 23:20, 5 August 2016

OCA — Fri, 05 Aug 2016 23:20:14 GMT

←Older revision		Revision as of 23:20, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism==		==Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism==
	<StructureSection load='2zmj' size='340' side='right' caption='[[2zmj]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='2zmj' size='340' side='right' caption='[[2zmj]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zmj]] 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=2ZMJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZMJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zmj]] 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=2ZMJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZMJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MI4:(1R,3R,7E,17BETA)-17-{(1S,2E,5R)-5-HYDROXY-1-METHYL-6-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]HEX-2-EN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>MI4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MI4:(1R,3R,7E,17BETA)-17-{(1S,2E,5R)-5-HYDROXY-1-METHYL-6-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]HEX-2-EN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>MI4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zmh\|2zmh]], [[2zmi\|2zmi]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zmh\|2zmh]], [[2zmi\|2zmi]]</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=2zmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zmj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zmj RCSB], [http://www.ebi.ac.uk/pdbsum/2zmj 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=2zmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zmj OCA], [http://pdbe.org/2zmj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zmj RCSB], [http://www.ebi.ac.uk/pdbsum/2zmj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zmj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2zmj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 29:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2zmj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rattus norvegicus~~]]	+	[[Category: Buffalo rat]]
	[[Category: DeLuca, H F]]		[[Category: DeLuca, H F]]
	[[Category: Igarashi, M]]		[[Category: Igarashi, M]]

OCA at 22:48, 25 December 2014

OCA — Thu, 25 Dec 2014 22:48:21 GMT

←Older revision		Revision as of 22:48, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2zmj]] 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=2ZMJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZMJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[2zmj]] 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=2ZMJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZMJ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MI4:(1R,3R,7E,17BETA)-17-{(1S,2E,5R)-5-HYDROXY-1-METHYL-6-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]HEX-2-EN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>MI4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MI4:(1R,3R,7E,17BETA)-17-{(1S,2E,5R)-5-HYDROXY-1-METHYL-6-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]HEX-2-EN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>MI4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zmh\|2zmh]], [[2zmi\|2zmi]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zmh\|2zmh]], [[2zmi\|2zmi]]</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=2zmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zmj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zmj RCSB], [http://www.ebi.ac.uk/pdbsum/2zmj 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=2zmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zmj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zmj RCSB], [http://www.ebi.ac.uk/pdbsum/2zmj 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_XENTR MED1_XENTR]] 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 (By similarity).
	== 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: DeLuca, H F.]]	+	[[Category: DeLuca, H F]]
-	[[Category: Igarashi, M.]]	+	[[Category: Igarashi, M]]
-	[[Category: Ikura, T.]]	+	[[Category: Ikura, T]]
-	[[Category: Ito, N.]]	+	[[Category: Ito, N]]
-	[[Category: Makishima, M.]]	+	[[Category: Makishima, M]]
-	[[Category: Nakabayashi, M.]]	+	[[Category: Nakabayashi, M]]
-	[[Category: Shimizu, M.]]	+	[[Category: Shimizu, M]]
-	[[Category: Tanaka, T.]]	+	[[Category: Tanaka, T]]
-	[[Category: Tokiwa, H.]]	+	[[Category: Tokiwa, H]]
-	[[Category: Yamada, S.]]	+	[[Category: Yamada, S]]
-	[[Category: Yoshimoto, N.]]	+	[[Category: Yoshimoto, N]]
	[[Category: Activator]]		[[Category: Activator]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]

OCA at 05:38, 2 October 2014

OCA — Thu, 02 Oct 2014 05:38:25 GMT

←Older revision		Revision as of 05:38, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2zmj.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism==
		+	<StructureSection load='2zmj' size='340' side='right' caption='[[2zmj]], [[Resolution\|resolution]] 2.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2zmj]] 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=2ZMJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZMJ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MI4:(1R,3R,7E,17BETA)-17-{(1S,2E,5R)-5-HYDROXY-1-METHYL-6-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]HEX-2-EN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>MI4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zmh\|2zmh]], [[2zmi\|2zmi]]</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=2zmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zmj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zmj RCSB], [http://www.ebi.ac.uk/pdbsum/2zmj 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/zm/2zmj_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 ==
		+	The X-ray crystal structures of the rat VDR ligand-binding domain complexed with 19-norvitamin D compounds that contain an adamantyl substituent at the side-chain terminus, 2a (ADTT), 2b (ADNY), and 2c (ADMI4) and a coactivator peptide derived from DRIP205 are reported. These compounds show a series of partial agonistic (10-75% efficacy)/antagonistic activities. All of these complexed receptors are crystallized in the canonical active conformation, regardless of their activity profiles. The bulky adamantyl side chain does not crowd helix 12 but protrudes into the gap formed by helix 11, loop 11-12, helix 3, and loop 6-7, thereby widening the ligand binding pocket. We suggest that these structural changes destabilize the active protein conformation and reduce its contribution to equilibrium among the active and inactive conformations. The coactivator peptide traps the minor active conformation, and the equilibrium shifts to the active conformation. As a result, these ligands show partial agonistic activities.

-	~~{{STRUCTURE_2zmj\| PDB=2zmj \| SCENE= }}~~	+	Crystal Structures of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and Partial Agonism.,Nakabayashi M, Yamada S, Yoshimoto N, Tanaka T, Igarashi M, Ikura T, Ito N, Makishima M, Tokiwa H, Deluca HF, Shimizu M J Med Chem. 2008 Aug 19. PMID:18710208<ref>PMID:18710208</ref>

-	~~===Crystal Structure~~ of ~~Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and~~/~~or Partial Agonism===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_18710208}}~~	+	==See Also==
-		+	*[[Sandbox vdr\|Sandbox vdr]]
-	==~~About this Structure~~==	+	*[[Vitamin D receptor\|Vitamin D receptor]]
-	[[~~2zmj~~]] ~~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=2ZMJ OCA~~].	+	== References ==
-		+	<references/>
-	==~~Reference~~==	+	__TOC__
-	<~~ref group="xtra">PMID:018710208<~~/~~ref~~><~~references group="xtra"~~/>	+	</StructureSection>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: DeLuca, H F.]]		[[Category: DeLuca, H F.]]

OCA: Protected "2zmj" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 23:14:06 GMT

Protected "2zmj" [edit=sysop:move=sysop]

←Older revision

Revision as of 23:14, 7 January 2013

OCA at 23:14, 7 January 2013

OCA — Mon, 07 Jan 2013 23:14:03 GMT

←Older revision		Revision as of 23:14, 7 January 2013
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-	{{Seed}}
	[[Image:2zmj.png\|left\|200px]]		[[Image:2zmj.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2zmj", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
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	{{STRUCTURE_2zmj\| PDB=2zmj \| SCENE= }}		{{STRUCTURE_2zmj\| PDB=2zmj \| SCENE= }}

	===Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism===		===Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18710208}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18710208 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_18710208}}		{{ABSTRACT_PUBMED_18710208}}

	==About this Structure==		==About this Structure==
-	~~2ZMJ~~ 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=2ZMJ OCA].	+	[[2zmj]] 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=2ZMJ OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18710208~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018710208</ref><references group="xtra"/>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: DeLuca, H F.]]		[[Category: DeLuca, H F.]]
Line 45:		Line 33:
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
-	[[Category: Zinc]]
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 10:08:36 2009''

OCA at 08:08, 18 February 2009

OCA — Wed, 18 Feb 2009 08:08:37 GMT

←Older revision		Revision as of 08:08, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2ZMJ 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=2ZMJ OCA].	+	2ZMJ 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=2ZMJ OCA].

	==Reference==		==Reference==
-	Crystal Structures of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and Partial Agonism., Nakabayashi M, Yamada S, Yoshimoto N, Tanaka T, Igarashi M, Ikura T, Ito N, Makishima M, Tokiwa H, Deluca HF, Shimizu M, J Med Chem. 2008 Aug 19. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18710208 18710208]~~	+	<ref group="xtra">PMID:18710208</ref><references group="xtra"/>
-	~~[[Category: Protein complex]]~~	+
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: DeLuca, H F.]]		[[Category: DeLuca, H F.]]
Line 49:		Line 48:
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Sep 17 13~~:08:~~53 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 10:08:36 2009''

OCA at 10:08, 17 September 2008

OCA — Wed, 17 Sep 2008 10:08:54 GMT

←Older revision		Revision as of 10:08, 17 September 2008
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	{{Seed}}		{{Seed}}
-	[[Image:2zmj.~~jpg~~\|left\|200px]]	+	[[Image:2zmj.png\|left\|200px]]

	<!--		<!--
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	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 3 13:10:16 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 17 13:08:53 2008''