2zxm - Revision history

OCA at 14:01, 1 November 2023

OCA — Wed, 01 Nov 2023 14:01:03 GMT

←Older revision		Revision as of 14:01, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='2zxm' size='340' side='right'caption='[[2zxm]], [[Resolution\|resolution]] 3.01Å' scene=''>		<StructureSection load='2zxm' size='340' side='right'caption='[[2zxm]], [[Resolution\|resolution]] 3.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zxm]] 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=2ZXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZXM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zxm]] 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=2ZXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZXM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JB1:(1R,3S,5Z)-5-[(2E)-2-[(1R,3AS,7AR)-1-[(2R,3S)-3-(2-HYDROXYETHYL)HEPTAN-2-YL]-7A-METHYL-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLIDENE]-4-METHYLIDENE-CYCLOHEXANE-1,3-DIOL'>JB1</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]] 3.01Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2zxn\|2zxn]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JB1:(1R,3S,5Z)-5-[(2E)-2-[(1R,3AS,7AR)-1-[(2R,3S)-3-(2-HYDROXYETHYL)HEPTAN-2-YL]-7A-METHYL-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLIDENE]-4-METHYLIDENE-CYCLOHEXANE-1,3-DIOL'>JB1</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nr1i1, Vdr ([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=2zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zxm OCA], [https://pdbe.org/2zxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zxm RCSB], [https://www.ebi.ac.uk/pdbsum/2zxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zxm 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=2zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zxm OCA], [https://pdbe.org/2zxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zxm RCSB], [https://www.ebi.ac.uk/pdbsum/2zxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zxm 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]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Buffalo rat]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ikura, T~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: ~~Ito, N~~]]	+	[[Category: Xenopus tropicalis]]
-	[[Category: ~~Nakabayashi, M~~]]	+	[[Category: Ikura T]]
-	[[Category: ~~Activator~~]]	+	[[Category: Ito N]]
-	[[Category: ~~Dna-binding]]~~	+	[[Category: Nakabayashi M]]
-	~~[[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 16:10, 22 December 2021

OCA — Wed, 22 Dec 2021 16:10:14 GMT

←Older revision		Revision as of 16:10, 22 December 2021
Line 1:		Line 1:

	==A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket==		==A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket==
-	<StructureSection load='2zxm' size='340' side='right' caption='[[2zxm]], [[Resolution\|resolution]] 3.01Å' scene=''>	+	<StructureSection load='2zxm' size='340' side='right'caption='[[2zxm]], [[Resolution\|resolution]] 3.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zxm]] 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=2ZXM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2ZXM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zxm]] 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=2ZXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZXM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JB1:(1R,3S,5Z)-5-[(2E)-2-[(1R,3AS,7AR)-1-[(2R,3S)-3-(2-HYDROXYETHYL)HEPTAN-2-YL]-7A-METHYL-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLIDENE]-4-METHYLIDENE-CYCLOHEXANE-1,3-DIOL'>JB1</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JB1:(1R,3S,5Z)-5-[(2E)-2-[(1R,3AS,7AR)-1-[(2R,3S)-3-(2-HYDROXYETHYL)HEPTAN-2-YL]-7A-METHYL-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLIDENE]-4-METHYLIDENE-CYCLOHEXANE-1,3-DIOL'>JB1</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zxn\|2zxn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2zxn\|2zxn]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nr1i1, Vdr ([~~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">Nr1i1, Vdr ([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=2zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zxm OCA], [~~http~~://pdbe.org/2zxm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2zxm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2zxm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2zxm 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=2zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zxm OCA], [https://pdbe.org/2zxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zxm RCSB], [https://www.ebi.ac.uk/pdbsum/2zxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zxm 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]]
Line 33:		Line 33:
	==See Also==		==See Also==
	*[[Sandbox vdr\|Sandbox vdr]]		*[[Sandbox vdr\|Sandbox vdr]]
-	*[[Vitamin D receptor\|Vitamin D receptor]]	+	*[[Vitamin D receptor 3D structures\|Vitamin D receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
		+	[[Category: Large Structures]]
	[[Category: Ikura, T]]		[[Category: Ikura, T]]
	[[Category: Ito, N]]		[[Category: Ito, N]]

OCA at 07:33, 18 October 2018

OCA — Thu, 18 Oct 2018 07:33:32 GMT

←Older revision		Revision as of 07:33, 18 October 2018
Line 1:		Line 1:
		+
	==A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket==		==A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket==
	<StructureSection load='2zxm' size='340' side='right' caption='[[2zxm]], [[Resolution\|resolution]] 3.01Å' scene=''>		<StructureSection load='2zxm' size='340' side='right' caption='[[2zxm]], [[Resolution\|resolution]] 3.01Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zxn\|2zxn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zxn\|2zxn]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nr1i1, Vdr ([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">Nr1i1, Vdr ([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=2zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zxm OCA], [http://pdbe.org/2zxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zxm RCSB], [http://www.ebi.ac.uk/pdbsum/2zxm 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=2zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zxm OCA], [http://pdbe.org/2zxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zxm RCSB], [http://www.ebi.ac.uk/pdbsum/2zxm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zxm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zx/2zxm_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zx/2zxm_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 50:		Line 51:
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
		+	[[Category: Zinc]]
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

OCA at 06:53, 9 February 2016

OCA — Tue, 09 Feb 2016 06:53:51 GMT

←Older revision		Revision as of 06:53, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='2zxm' size='340' side='right' caption='[[2zxm]], [[Resolution\|resolution]] 3.01Å' scene=''>		<StructureSection load='2zxm' size='340' side='right' caption='[[2zxm]], [[Resolution\|resolution]] 3.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zxm]] 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=2ZXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZXM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zxm]] 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=2ZXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZXM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JB1:(1R,3S,5Z)-5-[(2E)-2-[(1R,3AS,7AR)-1-[(2R,3S)-3-(2-HYDROXYETHYL)HEPTAN-2-YL]-7A-METHYL-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLIDENE]-4-METHYLIDENE-CYCLOHEXANE-1,3-DIOL'>JB1</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JB1:(1R,3S,5Z)-5-[(2E)-2-[(1R,3AS,7AR)-1-[(2R,3S)-3-(2-HYDROXYETHYL)HEPTAN-2-YL]-7A-METHYL-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLIDENE]-4-METHYLIDENE-CYCLOHEXANE-1,3-DIOL'>JB1</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zxn\|2zxn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zxn\|2zxn]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nr1i1, Vdr ([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">Nr1i1, Vdr ([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=2zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zxm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zxm RCSB], [http://www.ebi.ac.uk/pdbsum/2zxm 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=2zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zxm OCA], [http://pdbe.org/2zxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zxm RCSB], [http://www.ebi.ac.uk/pdbsum/2zxm PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<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=2zxm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2zxm" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rattus norvegicus~~]]	+	[[Category: Buffalo rat]]
	[[Category: Ikura, T]]		[[Category: Ikura, T]]
	[[Category: Ito, N]]		[[Category: Ito, N]]

OCA at 05:11, 25 December 2014

OCA — Thu, 25 Dec 2014 05:11:03 GMT

←Older revision		Revision as of 05:11, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2zxm]] 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=2ZXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZXM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2zxm]] 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=2ZXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZXM FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JB1:(1R,3S,5Z)-5-[(2E)-2-[(1R,3AS,7AR)-1-[(2R,3S)-3-(2-HYDROXYETHYL)HEPTAN-2-YL]-7A-METHYL-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLIDENE]-4-METHYLIDENE-CYCLOHEXANE-1,3-DIOL'>JB1</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JB1:(1R,3S,5Z)-5-[(2E)-2-[(1R,3AS,7AR)-1-[(2R,3S)-3-(2-HYDROXYETHYL)HEPTAN-2-YL]-7A-METHYL-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLIDENE]-4-METHYLIDENE-CYCLOHEXANE-1,3-DIOL'>JB1</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zxn\|2zxn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zxn\|2zxn]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nr1i1, Vdr ([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">Nr1i1, Vdr ([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=2zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zxm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zxm RCSB], [http://www.ebi.ac.uk/pdbsum/2zxm 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=2zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zxm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zxm RCSB], [http://www.ebi.ac.uk/pdbsum/2zxm 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: Ikura, T.]]	+	[[Category: Ikura, T]]
-	[[Category: Ito, N.]]	+	[[Category: Ito, N]]
-	[[Category: Nakabayashi, M.]]	+	[[Category: Nakabayashi, M]]
	[[Category: Activator]]		[[Category: Activator]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]

OCA at 05:12, 2 October 2014

OCA — Thu, 02 Oct 2014 05:12:36 GMT

←Older revision		Revision as of 05:12, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2zxm.~~png~~\|~~left~~\|200px]]	+	==A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket==
		+	<StructureSection load='2zxm' size='340' side='right' caption='[[2zxm]], [[Resolution\|resolution]] 3.01Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2zxm]] 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=2ZXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZXM FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JB1:(1R,3S,5Z)-5-[(2E)-2-[(1R,3AS,7AR)-1-[(2R,3S)-3-(2-HYDROXYETHYL)HEPTAN-2-YL]-7A-METHYL-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLIDENE]-4-METHYLIDENE-CYCLOHEXANE-1,3-DIOL'>JB1</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zxn\|2zxn]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nr1i1, Vdr ([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=2zxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zxm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zxm RCSB], [http://www.ebi.ac.uk/pdbsum/2zxm 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/zx/2zxm_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 ==
		+	To identify novel vitamin D receptor (VDR) ligands that induce a novel architecture within the ligand-binding pocket (LBP), we have investigated eight 22-butyl-1alpha,24-dihydroxyvitamin D(3) derivatives (3-10), all having a butyl group as the branched alkyl side chain. We found that the 22S-butyl-20-epi-25,26,27-trinorvitamin D derivative 5 was a potent VDR agonist, whereas the corresponding compound 4 with the natural configuration at C(20) was a potent VDR antagonist. Analogues with the full vitamin D(3) side chain were less potent agonist, and whether they were agonists or antagonists depended on the 24-configuration. X-ray crystal structures demonstrated that the VDR-LBD accommodating the potent agonist 5 has an architecture wherein the lower side and the helix 11 side of the LBP is simply expanded relative to the canonical active-VDR situation; in contrast, the potent antagonist 4 induces an extra cavity to accommodate the branched moiety. This is the first report of a VDR antagonist that generates a new cavity to alter the canonical pocket structure of the ligand occupied VDR.

-	~~{{STRUCTURE_2zxm\| PDB=2zxm \| SCENE= }}~~	+	A New Class of Vitamin D Analogues that Induce Structural Rearrangement of the Ligand-Binding Pocket of the Receptor.,Inaba Y, Yoshimoto N, Sakamaki Y, Nakabayashi M, Ikura T, Tamamura H, Ito N, Shimizu M, Yamamoto K J Med Chem. 2009 Feb 4. PMID:19193059<ref>PMID:19193059</ref>

-	~~===A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement~~ of the ~~Ligand-binding Pocket===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_19193059}}~~	+	==See Also==
-		+	*[[Sandbox vdr\|Sandbox vdr]]
-	==~~About this Structure~~==	+	*[[Vitamin D receptor\|Vitamin D receptor]]
-	[[~~2zxm~~]] ~~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=2ZXM OCA~~].	+	== References ==
-		+	<references/>
-	==~~Reference~~==	+	__TOC__
-	<~~ref group="xtra">PMID:019193059<~~/~~ref~~><~~references group="xtra"~~/>	+	</StructureSection>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Ikura, T.]]		[[Category: Ikura, T.]]

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

OCA — Mon, 07 Jan 2013 21:07:55 GMT

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

←Older revision

Revision as of 21:07, 7 January 2013

OCA at 21:07, 7 January 2013

OCA — Mon, 07 Jan 2013 21:07:54 GMT

←Older revision		Revision as of 21:07, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2zxm.png\|left\|200px]]		[[Image:2zxm.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2zxm", 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_2zxm\| PDB=2zxm \| SCENE= }}		{{STRUCTURE_2zxm\| PDB=2zxm \| SCENE= }}

	===A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket===		===A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19193059}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19193059 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19193059}}		{{ABSTRACT_PUBMED_19193059}}

	==About this Structure==		==About this Structure==
-	~~2ZXM~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZXM OCA].	+	[[2zxm]] 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=2ZXM OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19193059~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019193059</ref><references group="xtra"/>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Ikura, T.]]		[[Category: Ikura, T.]]
Line 37:		Line 25:
	[[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 Sep 22 12:03:52 2010''

OCA at 08:54, 22 September 2010

OCA — Wed, 22 Sep 2010 08:54:53 GMT

←Older revision		Revision as of 08:54, 22 September 2010
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2ZXM 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=2ZXM OCA].	+	2ZXM is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZXM OCA].

	==Reference==		==Reference==
-	A New Class of Vitamin D Analogues that Induce Structural Rearrangement of the Ligand-Binding Pocket of the Receptor., Inaba Y, Yoshimoto N, Sakamaki Y, Nakabayashi M, Ikura T, Tamamura H, Ito N, Shimizu M, Yamamoto K, J Med Chem. 2009 Feb 4. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/19193059 19193059]~~	+	<ref group="xtra">PMID:19193059</ref><references group="xtra"/>
-	~~[[Category: Protein complex]]~~	+
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: ~~Pdbx_ordinal=~~, ~~<PDBx~~:~~audit_author~~.]]	+	[[Category: Ikura, T.]]
		+	[[Category: Ito, N.]]
		+	[[Category: Nakabayashi, M.]]
	[[Category: Activator]]		[[Category: Activator]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]
Line 39:		Line 40:
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Mar 25 21~~:01:~~26 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 12:03:52 2010''

OCA at 19:01, 25 March 2009

OCA — Wed, 25 Mar 2009 19:01:26 GMT

←Older revision		Revision as of 19:01, 25 March 2009
Line 20:		Line 20:

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

	==Reference==		==Reference==
-	~~<ref group="xtra">~~PMID:~~19193059<~~/~~ref><references group="xtra"~~/>	+	A New Class of Vitamin D Analogues that Induce Structural Rearrangement of the Ligand-Binding Pocket of the Receptor., Inaba Y, Yoshimoto N, Sakamaki Y, Nakabayashi M, Ikura T, Tamamura H, Ito N, Shimizu M, Yamamoto K, J Med Chem. 2009 Feb 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19193059 19193059]
		+	[[Category: Protein complex]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: ~~Ikura~~, ~~T.]]~~	+	[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
-	~~[[Category~~: ~~Ito, N.]]~~	+
-	~~[[Category: Nakabayashi, M~~.]]	+
	[[Category: Activator]]		[[Category: Activator]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]
Line 40:		Line 39:
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 25 11:25:53 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 25 21:01:26 2009''