1nrl - Revision history

OCA at 07:59, 14 February 2024

OCA — Wed, 14 Feb 2024 07:59:09 GMT

←Older revision		Revision as of 07:59, 14 February 2024
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	<StructureSection load='1nrl' size='340' side='right'caption='[[1nrl]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1nrl' size='340' side='right'caption='[[1nrl]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nrl]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NRL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1NRL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nrl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NRL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NRL FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SRL:[2~~-(3,~~5-DI-TERT-BUTYL-4-HYDROXY-PHENYL)-1-(DIETHOXY-PHOSPHORYL)-VINYL~~]~~-PHOSPHONIC+ACID+DIETHLYL+ESTER'>SRL</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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;'>[[1ilg\|1ilg]]~~, ~~[[1ilh\|1ilh~~]~~], [[1m13\|1m13]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SRL:[2-(3,5-DI-TERT-BUTYL-4-HYDROXY-PHENYL)-1-(DIETHOXY-PHOSPHORYL)-VINYL]-PHOSPHONIC+ACID+DIETHLYL+ESTER'>SRL</scene></td></tr>
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b>~~</td><td class="sblockDat">NR112 or PXR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=1nrl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nrl OCA], [https://pdbe.org/1nrl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nrl RCSB], [https://www.ebi.ac.uk/pdbsum/1nrl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nrl ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1nrl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nrl OCA], [~~http~~://pdbe.org/1nrl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1nrl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1nrl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1nrl ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NR1I2_HUMAN NR1I2_HUMAN]] Nuclear receptor that binds and is activated by variety of endogenous and xenobiotic compounds. Transcription factor that activates the transcription of multiple genes involved in the metabolism and secretion of potentially harmful xenobiotics, drugs and endogenous compounds. Activated by the antibiotic rifampicin and various plant metabolites, such as hyperforin, guggulipid, colupulone, and isoflavones. Response to specific ligands is species-specific. Activated by naturally occurring steroids, such as pregnenolone and progesterone. Binds to a response element in the promoters of the CYP3A4 and ABCB1/MDR1 genes.<ref>PMID:9727070</ref> <ref>PMID:11668216</ref> <ref>PMID:11297522</ref> <ref>PMID:19297428</ref> <ref>PMID:12578355</ref> <ref>PMID:18768384</ref>	+	[https://www.uniprot.org/uniprot/NR1I2_HUMAN NR1I2_HUMAN] Nuclear receptor that binds and is activated by variety of endogenous and xenobiotic compounds. Transcription factor that activates the transcription of multiple genes involved in the metabolism and secretion of potentially harmful xenobiotics, drugs and endogenous compounds. Activated by the antibiotic rifampicin and various plant metabolites, such as hyperforin, guggulipid, colupulone, and isoflavones. Response to specific ligands is species-specific. Activated by naturally occurring steroids, such as pregnenolone and progesterone. Binds to a response element in the promoters of the CYP3A4 and ABCB1/MDR1 genes.<ref>PMID:9727070</ref> <ref>PMID:11668216</ref> <ref>PMID:11297522</ref> <ref>PMID:19297428</ref> <ref>PMID:12578355</ref> <ref>PMID:18768384</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1nrl 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=1nrl ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The pregnane X receptor (PXR) detects the presence of a wide variety of endogenous and xenobiotic compounds, and is a master regulator of the expression of genes central to drug metabolism and excretion. We present the 2.0A crystal structure of the human PXR ligand-binding domain (LBD) in complex with the cholesterol-lowering compound SR12813 and a 25 amino acid residue fragment of the human steroid receptor coactivator-1 (SRC-1) containing one LXXLL motif. PXR crystallizes as a homodimer in the asymmetric unit in this structure and possesses a novel alpha2 helix adjacent to its ligand-binding cavity. The SRC-1 peptide forms two distinct helices and binds adjacent to the ligand-dependent transactivation AF-2 helix on the surface of PXR. In contrast with previous PXR structures, in which SR12813 bound in multiple orientations, the small SR12813 agonist in this structure binds in a single, unique orientation within the receptor's ligand-binding pocket and contacts the AF-2 helix. Thermal denaturation studies reveal that the SR12813 ligand and SRC-1 coactivator peptide each stabilize the LBD of PXR, and that together they exert an additive effect on the stability of the receptor. These results indicate that the binding of coactivator to the surface of PXR limits the ability of this promiscuous receptor to "breathe" and helps to trap a single, active conformation of SR12813. They further reveal that specificity is required for PXR activation.
-
-	Coactivator binding promotes the specific interaction between ligand and the pregnane X receptor.,Watkins RE, Davis-Searles PR, Lambert MH, Redinbo MR J Mol Biol. 2003 Aug 22;331(4):815-28. PMID:12909012<ref>PMID:12909012</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1nrl" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Pregnane X receptor\|Pregnane X receptor]]	+	*[[Pregnane X receptor 3D structures\|Pregnane X receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Davis-Searles~~, P R~~]]	+	[[Category: Davis-Searles PR]]
-	[[Category: Lambert~~, M H~~]]	+	[[Category: Lambert MH]]
-	[[Category: Redinbo~~, M R~~]]	+	[[Category: Redinbo MR]]
-	[[Category: Watkins~~, R E]]~~	+	[[Category: Watkins RE]]
-	~~[[Category: Coactivator]]~~	+
-	~~[[Category: Ligand binding domain]]~~	+
-	~~[[Category: Nuclear receptor]]~~	+
-	~~[[Category: Pxr]]~~	+
-	~~[[Category: Src-1]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Xenobiotic~~]]	+

OCA at 08:56, 2 December 2020

OCA — Wed, 02 Dec 2020 08:56:09 GMT

←Older revision		Revision as of 08:56, 2 December 2020
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	==Crystal Structure of the human PXR-LBD in complex with an SRC-1 coactivator peptide and SR12813==		==Crystal Structure of the human PXR-LBD in complex with an SRC-1 coactivator peptide and SR12813==
-	<StructureSection load='1nrl' size='340' side='right' caption='[[1nrl]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1nrl' size='340' side='right'caption='[[1nrl]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nrl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NRL OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1NRL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nrl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NRL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1NRL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SRL:[2-(3,5-DI-TERT-BUTYL-4-HYDROXY-PHENYL)-1-(DIETHOXY-PHOSPHORYL)-VINYL]-PHOSPHONIC+ACID+DIETHLYL+ESTER'>SRL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SRL:[2-(3,5-DI-TERT-BUTYL-4-HYDROXY-PHENYL)-1-(DIETHOXY-PHOSPHORYL)-VINYL]-PHOSPHONIC+ACID+DIETHLYL+ESTER'>SRL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ilg\|1ilg]], [[1ilh\|1ilh]], [[1m13\|1m13]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ilg\|1ilg]], [[1ilh\|1ilh]], [[1m13\|1m13]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NR112 or PXR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NR112 or PXR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=1nrl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nrl OCA], [http://pdbe.org/1nrl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nrl RCSB], [http://www.ebi.ac.uk/pdbsum/1nrl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nrl ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1nrl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nrl OCA], [http://pdbe.org/1nrl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nrl RCSB], [http://www.ebi.ac.uk/pdbsum/1nrl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nrl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1nrl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1nrl" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Pregnane X receptor\|Pregnane X receptor]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Davis-Searles, P R]]		[[Category: Davis-Searles, P R]]
	[[Category: Lambert, M H]]		[[Category: Lambert, M H]]

OCA at 07:06, 7 February 2018

OCA — Wed, 07 Feb 2018 07:06:19 GMT

←Older revision		Revision as of 07:06, 7 February 2018
Line 1:		Line 1:
		+
	==Crystal Structure of the human PXR-LBD in complex with an SRC-1 coactivator peptide and SR12813==		==Crystal Structure of the human PXR-LBD in complex with an SRC-1 coactivator peptide and SR12813==
	<StructureSection load='1nrl' size='340' side='right' caption='[[1nrl]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1nrl' size='340' side='right' caption='[[1nrl]], [[Resolution\|resolution]] 2.00Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ilg\|1ilg]], [[1ilh\|1ilh]], [[1m13\|1m13]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ilg\|1ilg]], [[1ilh\|1ilh]], [[1m13\|1m13]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NR112 or PXR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NR112 or PXR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=1nrl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nrl OCA], [http://pdbe.org/1nrl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nrl RCSB], [http://www.ebi.ac.uk/pdbsum/1nrl 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=1nrl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nrl OCA], [http://pdbe.org/1nrl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nrl RCSB], [http://www.ebi.ac.uk/pdbsum/1nrl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nrl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nr/1nrl_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nr/1nrl_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 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1nrl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1nrl" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Pregnane X receptor\|Pregnane X receptor]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:59, 10 February 2016

OCA — Wed, 10 Feb 2016 05:59:42 GMT

←Older revision		Revision as of 05:59, 10 February 2016
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=1nrl ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:03, 11 September 2015

OCA — Fri, 11 Sep 2015 06:03:17 GMT

←Older revision		Revision as of 06:03, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1nrl' size='340' side='right' caption='[[1nrl]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1nrl' size='340' side='right' caption='[[1nrl]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nrl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NRL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NRL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nrl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NRL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NRL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SRL:[2-(3,5-DI-TERT-BUTYL-4-HYDROXY-PHENYL)-1-(DIETHOXY-PHOSPHORYL)-VINYL]-PHOSPHONIC+ACID+DIETHLYL+ESTER'>SRL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SRL:[2-(3,5-DI-TERT-BUTYL-4-HYDROXY-PHENYL)-1-(DIETHOXY-PHOSPHORYL)-VINYL]-PHOSPHONIC+ACID+DIETHLYL+ESTER'>SRL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ilg\|1ilg]], [[1ilh\|1ilh]], [[1m13\|1m13]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ilg\|1ilg]], [[1ilh\|1ilh]], [[1m13\|1m13]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NR112 or PXR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NR112 or PXR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=1nrl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nrl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nrl RCSB], [http://www.ebi.ac.uk/pdbsum/1nrl 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=1nrl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nrl OCA], [http://pdbe.org/1nrl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nrl RCSB], [http://www.ebi.ac.uk/pdbsum/1nrl PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 1nrl" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Davis-Searles, P R]]		[[Category: Davis-Searles, P R]]
	[[Category: Lambert, M H]]		[[Category: Lambert, M H]]

OCA at 12:18, 25 December 2014

OCA — Thu, 25 Dec 2014 12:18:03 GMT

←Older revision		Revision as of 12:18, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1nrl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NRL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NRL FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nrl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NRL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NRL FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SRL:[2-(3,5-DI-TERT-BUTYL-4-HYDROXY-PHENYL)-1-(DIETHOXY-PHOSPHORYL)-VINYL]-PHOSPHONIC+ACID+DIETHLYL+ESTER'>SRL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SRL:[2-(3,5-DI-TERT-BUTYL-4-HYDROXY-PHENYL)-1-(DIETHOXY-PHOSPHORYL)-VINYL]-PHOSPHONIC+ACID+DIETHLYL+ESTER'>SRL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ilg\|1ilg]], [[1ilh\|1ilh]], [[1m13\|1m13]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ilg\|1ilg]], [[1ilh\|1ilh]], [[1m13\|1m13]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NR112 or PXR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NR112 or PXR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=1nrl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nrl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nrl RCSB], [http://www.ebi.ac.uk/pdbsum/1nrl 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=1nrl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nrl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nrl RCSB], [http://www.ebi.ac.uk/pdbsum/1nrl PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NR1I2_HUMAN NR1I2_HUMAN]] Nuclear receptor that binds and is activated by variety of endogenous and xenobiotic compounds. Transcription factor that activates the transcription of multiple genes involved in the metabolism and secretion of potentially harmful xenobiotics, drugs and endogenous compounds. Activated by the antibiotic rifampicin and various plant metabolites, such as hyperforin, guggulipid, colupulone, and isoflavones. Response to specific ligands is species-specific. Activated by naturally occurring steroids, such as pregnenolone and progesterone. Binds to a response element in the promoters of the CYP3A4 and ABCB1/MDR1 genes.<ref>PMID:9727070</ref> <ref>PMID:11668216</ref> <ref>PMID:11297522</ref> <ref>PMID:19297428</ref> <ref>PMID:12578355</ref> <ref>PMID:18768384</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Davis-Searles, P R.]]	+	[[Category: Davis-Searles, P R]]
-	[[Category: Lambert, M H.]]	+	[[Category: Lambert, M H]]
-	[[Category: Redinbo, M R.]]	+	[[Category: Redinbo, M R]]
-	[[Category: Watkins, R E.]]	+	[[Category: Watkins, R E]]
	[[Category: Coactivator]]		[[Category: Coactivator]]
	[[Category: Ligand binding domain]]		[[Category: Ligand binding domain]]

OCA at 14:58, 29 September 2014

OCA — Mon, 29 Sep 2014 14:58:04 GMT

←Older revision		Revision as of 14:58, 29 September 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1nrl\| PDB=1nrl \| SCENE= }}~~	+	==Crystal Structure of the human PXR-LBD in complex with an SRC-1 coactivator peptide and SR12813==
-	===Crystal Structure of the human PXR-LBD in complex with an SRC-1 coactivator peptide and SR12813===	+	<StructureSection load='1nrl' size='340' side='right' caption='[[1nrl]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~{{ABSTRACT_PUBMED_12909012}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1nrl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NRL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NRL FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SRL:[2-(3,5-DI-TERT-BUTYL-4-HYDROXY-PHENYL)-1-(DIETHOXY-PHOSPHORYL)-VINYL]-PHOSPHONIC+ACID+DIETHLYL+ESTER'>SRL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ilg\|1ilg]], [[1ilh\|1ilh]], [[1m13\|1m13]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NR112 or PXR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=1nrl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nrl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nrl RCSB], [http://www.ebi.ac.uk/pdbsum/1nrl 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/nr/1nrl_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 pregnane X receptor (PXR) detects the presence of a wide variety of endogenous and xenobiotic compounds, and is a master regulator of the expression of genes central to drug metabolism and excretion. We present the 2.0A crystal structure of the human PXR ligand-binding domain (LBD) in complex with the cholesterol-lowering compound SR12813 and a 25 amino acid residue fragment of the human steroid receptor coactivator-1 (SRC-1) containing one LXXLL motif. PXR crystallizes as a homodimer in the asymmetric unit in this structure and possesses a novel alpha2 helix adjacent to its ligand-binding cavity. The SRC-1 peptide forms two distinct helices and binds adjacent to the ligand-dependent transactivation AF-2 helix on the surface of PXR. In contrast with previous PXR structures, in which SR12813 bound in multiple orientations, the small SR12813 agonist in this structure binds in a single, unique orientation within the receptor's ligand-binding pocket and contacts the AF-2 helix. Thermal denaturation studies reveal that the SR12813 ligand and SRC-1 coactivator peptide each stabilize the LBD of PXR, and that together they exert an additive effect on the stability of the receptor. These results indicate that the binding of coactivator to the surface of PXR limits the ability of this promiscuous receptor to "breathe" and helps to trap a single, active conformation of SR12813. They further reveal that specificity is required for PXR activation.

-	~~==Function==~~	+	Coactivator binding promotes the specific interaction between ligand and the pregnane X receptor.,Watkins RE, Davis-Searles PR, Lambert MH, Redinbo MR J Mol Biol. 2003 Aug 22;331(4):815-28. PMID:12909012<ref>PMID:12909012</ref>
-	~~[[http://www.uniprot.org/uniprot/NR1I2_HUMAN NR1I2_HUMAN]] Nuclear receptor that binds~~ and ~~is activated by variety of endogenous and xenobiotic compounds. Transcription factor that activates~~ the ~~transcription of multiple genes involved in the metabolism and secretion of potentially harmful xenobiotics, drugs and endogenous compounds~~. ~~Activated by the antibiotic rifampicin and various plant metabolites~~, ~~such as hyperforin~~, ~~guggulipid~~, ~~colupulone~~, ~~and isoflavones~~. ~~Response to specific ligands is species~~-~~specific~~. ~~Activated by naturally occurring steroids, such as pregnenolone and progesterone. Binds to a response element in the promoters of the CYP3A4 and ABCB1/MDR1 genes.<ref>~~PMID:~~9727070</ref><ref>PMID:11668216</ref><ref>PMID:11297522</ref><ref>PMID:19297428</ref><ref>PMID:12578355</ref>~~<ref>PMID:~~18768384~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[1nrl]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1NRL OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:012909012</ref><ref group~~=~~"xtra">PMID:012740396</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Pregnane X receptor\|Pregnane X receptor]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Davis-Searles, P R.]]		[[Category: Davis-Searles, P R.]]

OCA at 01:09, 25 March 2013

OCA — Mon, 25 Mar 2013 01:09:30 GMT

←Older revision		Revision as of 01:09, 25 March 2013
Line 1:		Line 1:
-	[[Image:1nrl.png\|left\|200px]]
-
	{{STRUCTURE_1nrl\| PDB=1nrl \| SCENE= }}		{{STRUCTURE_1nrl\| PDB=1nrl \| SCENE= }}
-
	===Crystal Structure of the human PXR-LBD in complex with an SRC-1 coactivator peptide and SR12813===		===Crystal Structure of the human PXR-LBD in complex with an SRC-1 coactivator peptide and SR12813===
		+	{{ABSTRACT_PUBMED_12909012}}

-	~~{{ABSTRACT_PUBMED_12909012}}~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/NR1I2_HUMAN NR1I2_HUMAN]] Nuclear receptor that binds and is activated by variety of endogenous and xenobiotic compounds. Transcription factor that activates the transcription of multiple genes involved in the metabolism and secretion of potentially harmful xenobiotics, drugs and endogenous compounds. Activated by the antibiotic rifampicin and various plant metabolites, such as hyperforin, guggulipid, colupulone, and isoflavones. Response to specific ligands is species-specific. Activated by naturally occurring steroids, such as pregnenolone and progesterone. Binds to a response element in the promoters of the CYP3A4 and ABCB1/MDR1 genes.<ref>PMID:9727070</ref><ref>PMID:11668216</ref><ref>PMID:11297522</ref><ref>PMID:19297428</ref><ref>PMID:12578355</ref><ref>PMID:18768384</ref>

	==About this Structure==		==About this Structure==
Line 11:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:012909012</ref><ref group="xtra">PMID:012740396</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012909012</ref><ref group="xtra">PMID:012740396</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Davis-Searles, P R.]]		[[Category: Davis-Searles, P R.]]

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

OCA — Wed, 05 Dec 2012 19:43:41 GMT

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

←Older revision

Revision as of 19:43, 5 December 2012

OCA at 19:43, 5 December 2012

OCA — Wed, 05 Dec 2012 19:43:39 GMT

←Older revision		Revision as of 19:43, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1nrl.png\|left\|200px]]		[[Image:1nrl.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1nrl", 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_1nrl\| PDB=1nrl \| SCENE= }}		{{STRUCTURE_1nrl\| PDB=1nrl \| SCENE= }}

	===Crystal Structure of the human PXR-LBD in complex with an SRC-1 coactivator peptide and SR12813===		===Crystal Structure of the human PXR-LBD in complex with an SRC-1 coactivator peptide and SR12813===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12909012}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12909012 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12909012}}		{{ABSTRACT_PUBMED_12909012}}

	==About this Structure==		==About this Structure==
-	~~1NRL~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NRL OCA].	+	[[1nrl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NRL OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12909012~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012909012</ref><ref group="xtra">PMID:012740396</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Davis-Searles, P R.]]		[[Category: Davis-Searles, P R.]]
Line 34:		Line 22:
	[[Category: Pxr]]		[[Category: Pxr]]
	[[Category: Src-1]]		[[Category: Src-1]]
		+	[[Category: Transcription]]
	[[Category: Xenobiotic]]		[[Category: Xenobiotic]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:58:35 2009''