4nqa - Revision history

OCA at 12:34, 1 March 2024

2024-03-01T12:34:51Z

←Older revision		Revision as of 12:34, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4nqa]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NQA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NQA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4nqa]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NQA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NQA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=965:[3-(3-{[2-CHLORO-3-(TRIFLUOROMETHYL)BENZYL](2,2-DIPHENYLETHYL)AMINO}PROPOXY)PHENYL]ACETIC+ACID'>965</scene>, <scene name='pdbligand=9CR:(9CIS)-RETINOIC+ACID'>9CR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3.102Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=965:[3-(3-{[2-CHLORO-3-(TRIFLUOROMETHYL)BENZYL](2,2-DIPHENYLETHYL)AMINO}PROPOXY)PHENYL]ACETIC+ACID'>965</scene>, <scene name='pdbligand=9CR:(9CIS)-RETINOIC+ACID'>9CR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=4nqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nqa OCA], [https://pdbe.org/4nqa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nqa RCSB], [https://www.ebi.ac.uk/pdbsum/4nqa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nqa 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=4nqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nqa OCA], [https://pdbe.org/4nqa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nqa RCSB], [https://www.ebi.ac.uk/pdbsum/4nqa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nqa ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/RXRA_HUMAN RXRA_HUMAN] Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for RXRs is 9-cis retinoic acid. RXRA serves as a common heterodimeric partner for a number of nuclear receptors. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation, chromatin condensation and transcriptional suppression. On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation. The RXRA/PPARA heterodimer is required for PPARA transcriptional activity on fatty acid oxidation genes such as ACOX1 and the P450 system genes.<ref>PMID:10195690</ref> <ref>PMID:11162439</ref> <ref>PMID:11915042</ref> <ref>PMID:20215566</ref>		[https://www.uniprot.org/uniprot/RXRA_HUMAN RXRA_HUMAN] Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for RXRs is 9-cis retinoic acid. RXRA serves as a common heterodimeric partner for a number of nuclear receptors. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation, chromatin condensation and transcriptional suppression. On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation. The RXRA/PPARA heterodimer is required for PPARA transcriptional activity on fatty acid oxidation genes such as ACOX1 and the P450 system genes.<ref>PMID:10195690</ref> <ref>PMID:11162439</ref> <ref>PMID:11915042</ref> <ref>PMID:20215566</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Nuclear receptors (NRs) are conditional transcription factors with common multidomain organization that bind diverse DNA elements. How DNA sequences influence NR conformation is poorly understood. Here we report the crystal structure of the human retinoid X receptor alpha-liver X receptor beta (RXRalpha-LXRbeta) heterodimer on its cognate element, an AGGTCA direct repeat spaced by 4 nt. The complex has an extended X-shaped arrangement, with DNA- and ligand-binding domains crossed, in contrast to the parallel domain arrangement of other NRs that bind an AGGTCA direct repeat spaced by 1 nt. The LXRbeta core binds DNA via canonical contacts and auxiliary DNA contacts that enhance affinity for the response element. Comparisons of RXRalpha-LXRbetas in the crystal asymmetric unit and with previous NR structures reveal flexibility in NR organization and suggest a role for RXRalpha in adaptation of heterodimeric complexes to DNA.
-
-	Structure of the retinoid X receptor alpha-liver X receptor beta (RXRalpha-LXRbeta) heterodimer on DNA.,Lou X, Toresson G, Benod C, Suh JH, Philips KJ, Webb P, Gustafsson JA Nat Struct Mol Biol. 2014 Mar;21(3):277-81. doi: 10.1038/nsmb.2778. Epub 2014 Feb, 23. PMID:24561505<ref>PMID:24561505</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4nqa" style="background-color:#fffaf0;"></div>

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

OCA at 08:42, 11 January 2023

2023-01-11T08:42:17Z

←Older revision		Revision as of 08:42, 11 January 2023
Line 3:		Line 3:
	<StructureSection load='4nqa' size='340' side='right'caption='[[4nqa]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4nqa' size='340' side='right'caption='[[4nqa]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4nqa]] is a 12 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=4NQA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4NQA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4nqa]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NQA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NQA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=965:[3-(3-{[2-CHLORO-3-(TRIFLUOROMETHYL)BENZYL](2,2-DIPHENYLETHYL)AMINO}PROPOXY)PHENYL]ACETIC+ACID'>965</scene>, <scene name='pdbligand=9CR:(9CIS)-RETINOIC+ACID'>9CR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=965:[3-(3-{[2-CHLORO-3-(TRIFLUOROMETHYL)BENZYL](2,2-DIPHENYLETHYL)AMINO}PROPOXY)PHENYL]ACETIC+ACID'>965</scene>, <scene name='pdbligand=9CR:(9CIS)-RETINOIC+ACID'>9CR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RXRA, NR2B1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), NR1H2, hCG_22944 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), NCOA2, BHLHE75, TIF2 ([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=4nqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nqa OCA], [https://pdbe.org/4nqa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nqa RCSB], [https://www.ebi.ac.uk/pdbsum/4nqa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nqa ProSAT]</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=4nqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nqa OCA], [~~http~~://pdbe.org/4nqa PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4nqa RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4nqa PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4nqa ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Disease ==
-	[[http://www.uniprot.org/uniprot/NCOA2_HUMAN NCOA2_HUMAN]] Note=Chromosomal aberrations involving NCOA2 may be a cause of acute myeloid leukemias. Inversion inv(8)(p11;q13) generates the KAT6A-NCOA2 oncogene, which consists of the N-terminal part of KAT6A and the C-terminal part of NCOA2/TIF2. KAT6A-NCOA2 binds to CREBBP and disrupts its function in transcription activation.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RXRA_HUMAN RXRA_HUMAN]] Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for RXRs is 9-cis retinoic acid. RXRA serves as a common heterodimeric partner for a number of nuclear receptors. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation, chromatin condensation and transcriptional suppression. On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation. The RXRA/PPARA heterodimer is required for PPARA transcriptional activity on fatty acid oxidation genes such as ACOX1 and the P450 system genes.<ref>PMID:10195690</ref> <ref>PMID:11162439</ref> <ref>PMID:11915042</ref> <ref>PMID:20215566</ref> [[http://www.uniprot.org/uniprot/NCOA2_HUMAN NCOA2_HUMAN]] Transcriptional coactivator for steroid receptors and nuclear receptors. Coactivator of the steroid binding domain (AF-2) but not of the modulating N-terminal domain (AF-1). Required with NCOA1 to control energy balance between white and brown adipose tissues.<ref>PMID:9430642</ref>	+	[https://www.uniprot.org/uniprot/RXRA_HUMAN RXRA_HUMAN] Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for RXRs is 9-cis retinoic acid. RXRA serves as a common heterodimeric partner for a number of nuclear receptors. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation, chromatin condensation and transcriptional suppression. On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation. The RXRA/PPARA heterodimer is required for PPARA transcriptional activity on fatty acid oxidation genes such as ACOX1 and the P450 system genes.<ref>PMID:10195690</ref> <ref>PMID:11162439</ref> <ref>PMID:11915042</ref> <ref>PMID:20215566</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 21:
	==See Also==		==See Also==
	*[[Liver X receptor\|Liver X receptor]]		*[[Liver X receptor\|Liver X receptor]]
-	*[[Retinoid X receptor\|Retinoid X receptor]]	+	*[[Retinoid X receptor 3D structures\|Retinoid X receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Benod, C]]	+	[[Category: Synthetic construct]]
-	[[Category: Gustafsson~~, J A~~]]	+	[[Category: Benod C]]
-	[[Category: Lou~~, X H~~]]	+	[[Category: Gustafsson JA]]
-	[[Category: Phillips~~, K J~~]]	+	[[Category: Lou XH]]
-	[[Category: Suh~~, J H~~]]	+	[[Category: Phillips KJ]]
-	[[Category: Toresson, G]]	+	[[Category: Suh JH]]
-	[[Category: Webb, P]]	+	[[Category: Toresson G]]
-	~~[[Category: Dbd]]~~	+	[[Category: Webb P]]
-	~~[[Category: Lbd]]~~	+
-	~~[[Category: Ligand]]~~	+
-	~~[[Category: Lxr]]~~	+
-	~~[[Category: Multi-domain]]~~	+
-	~~[[Category: Rxr]]~~	+
-	~~[[Category: Transcription regulator-dna complex]]~~	+
-	~~[[Category: Zinc finger~~]]	+

OCA at 08:09, 10 April 2019

2019-04-10T08:09:09Z

←Older revision		Revision as of 08:09, 10 April 2019
Line 1:		Line 1:

	==Crystal structure of liganded hRXR-alpha/hLXR-beta heterodimer on DNA==		==Crystal structure of liganded hRXR-alpha/hLXR-beta heterodimer on DNA==
-	<StructureSection load='4nqa' size='340' side='right' caption='[[4nqa]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='4nqa' size='340' side='right'caption='[[4nqa]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4nqa]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NQA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NQA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4nqa]] is a 12 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=4NQA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NQA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=965:[3-(3-{[2-CHLORO-3-(TRIFLUOROMETHYL)BENZYL](2,2-DIPHENYLETHYL)AMINO}PROPOXY)PHENYL]ACETIC+ACID'>965</scene>, <scene name='pdbligand=9CR:(9CIS)-RETINOIC+ACID'>9CR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=965:[3-(3-{[2-CHLORO-3-(TRIFLUOROMETHYL)BENZYL](2,2-DIPHENYLETHYL)AMINO}PROPOXY)PHENYL]ACETIC+ACID'>965</scene>, <scene name='pdbligand=9CR:(9CIS)-RETINOIC+ACID'>9CR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RXRA, NR2B1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), NR1H2, hCG_22944 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), NCOA2, BHLHE75, TIF2 ([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=4nqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nqa OCA], [http://pdbe.org/4nqa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nqa RCSB], [http://www.ebi.ac.uk/pdbsum/4nqa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nqa ProSAT]</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=4nqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nqa OCA], [http://pdbe.org/4nqa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nqa RCSB], [http://www.ebi.ac.uk/pdbsum/4nqa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nqa ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:

	==See Also==		==See Also==
		+	*[[Liver X receptor\|Liver X receptor]]
	*[[Retinoid X receptor\|Retinoid X receptor]]		*[[Retinoid X receptor\|Retinoid X receptor]]
	== References ==		== References ==
Line 27:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Benod, C]]		[[Category: Benod, C]]
	[[Category: Gustafsson, J A]]		[[Category: Gustafsson, J A]]

OCA at 20:03, 9 December 2016

2016-12-09T20:03:13Z

←Older revision		Revision as of 20:03, 9 December 2016
Line 3:		Line 3:
	<StructureSection load='4nqa' size='340' side='right' caption='[[4nqa]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4nqa' size='340' side='right' caption='[[4nqa]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4nqa]] is a 12 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=4NQA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NQA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4nqa]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NQA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NQA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=965:[3-(3-{[2-CHLORO-3-(TRIFLUOROMETHYL)BENZYL](2,2-DIPHENYLETHYL)AMINO}PROPOXY)PHENYL]ACETIC+ACID'>965</scene>, <scene name='pdbligand=~~REA~~:RETINOIC+ACID'>~~REA~~</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=965:[3-(3-{[2-CHLORO-3-(TRIFLUOROMETHYL)BENZYL](2,2-DIPHENYLETHYL)AMINO}PROPOXY)PHENYL]ACETIC+ACID'>965</scene>, <scene name='pdbligand=9CR:(9CIS)-RETINOIC+ACID'>9CR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RXRA, NR2B1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), NR1H2, hCG_22944 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), NCOA2, BHLHE75, TIF2 ([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=4nqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nqa OCA], [http://pdbe.org/4nqa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nqa RCSB], [http://www.ebi.ac.uk/pdbsum/4nqa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nqa ProSAT]</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=4nqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nqa OCA], [http://pdbe.org/4nqa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nqa RCSB], [http://www.ebi.ac.uk/pdbsum/4nqa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nqa ProSAT]</span></td></tr>
	</table>		</table>
Line 28:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Human]]
	[[Category: Benod, C]]		[[Category: Benod, C]]
	[[Category: Gustafsson, J A]]		[[Category: Gustafsson, J A]]

OCA at 16:47, 11 August 2016

2016-08-11T16:47:46Z

←Older revision		Revision as of 16:47, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of liganded hRXR-alpha/hLXR-beta heterodimer on DNA==		==Crystal structure of liganded hRXR-alpha/hLXR-beta heterodimer on DNA==
	<StructureSection load='4nqa' size='340' side='right' caption='[[4nqa]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4nqa' size='340' side='right' caption='[[4nqa]], [[Resolution\|resolution]] 3.10Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=965:[3-(3-{[2-CHLORO-3-(TRIFLUOROMETHYL)BENZYL](2,2-DIPHENYLETHYL)AMINO}PROPOXY)PHENYL]ACETIC+ACID'>965</scene>, <scene name='pdbligand=REA:RETINOIC+ACID'>REA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=965:[3-(3-{[2-CHLORO-3-(TRIFLUOROMETHYL)BENZYL](2,2-DIPHENYLETHYL)AMINO}PROPOXY)PHENYL]ACETIC+ACID'>965</scene>, <scene name='pdbligand=REA:RETINOIC+ACID'>REA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RXRA, NR2B1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), NR1H2, hCG_22944 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), NCOA2, BHLHE75, TIF2 ([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">RXRA, NR2B1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), NR1H2, hCG_22944 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), NCOA2, BHLHE75, TIF2 ([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=4nqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nqa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nqa RCSB], [http://www.ebi.ac.uk/pdbsum/4nqa 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=4nqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nqa OCA], [http://pdbe.org/4nqa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nqa RCSB], [http://www.ebi.ac.uk/pdbsum/4nqa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nqa ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 19:		Line 20:
	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 4nqa" style="background-color:#fffaf0;"></div>

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

OCA at 09:09, 5 January 2015

2015-01-05T09:09:54Z

←Older revision		Revision as of 09:09, 5 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4nqa\| PDB=4nqa \| SCENE= }}~~	+	==Crystal structure of liganded hRXR-alpha/hLXR-beta heterodimer on DNA==
-	===Crystal structure of liganded hRXR-alpha/hLXR-beta heterodimer on DNA===	+	<StructureSection load='4nqa' size='340' side='right' caption='[[4nqa]], [[Resolution\|resolution]] 3.10Å' scene=''>
-	{~~{ABSTRACT_PUBMED_24561505}~~}	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4nqa]] is a 12 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=4NQA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NQA FirstGlance]. <br>
-	==Disease==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=965:[3-(3-{[2-CHLORO-3-(TRIFLUOROMETHYL)BENZYL](2,2-DIPHENYLETHYL)AMINO}PROPOXY)PHENYL]ACETIC+ACID'>965</scene>, <scene name='pdbligand=REA:RETINOIC+ACID'>REA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RXRA, NR2B1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), NR1H2, hCG_22944 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), NCOA2, BHLHE75, TIF2 ([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=4nqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nqa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nqa RCSB], [http://www.ebi.ac.uk/pdbsum/4nqa PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
	[[http://www.uniprot.org/uniprot/NCOA2_HUMAN NCOA2_HUMAN]] Note=Chromosomal aberrations involving NCOA2 may be a cause of acute myeloid leukemias. Inversion inv(8)(p11;q13) generates the KAT6A-NCOA2 oncogene, which consists of the N-terminal part of KAT6A and the C-terminal part of NCOA2/TIF2. KAT6A-NCOA2 binds to CREBBP and disrupts its function in transcription activation.		[[http://www.uniprot.org/uniprot/NCOA2_HUMAN NCOA2_HUMAN]] Note=Chromosomal aberrations involving NCOA2 may be a cause of acute myeloid leukemias. Inversion inv(8)(p11;q13) generates the KAT6A-NCOA2 oncogene, which consists of the N-terminal part of KAT6A and the C-terminal part of NCOA2/TIF2. KAT6A-NCOA2 binds to CREBBP and disrupts its function in transcription activation.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RXRA_HUMAN RXRA_HUMAN]] Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for RXRs is 9-cis retinoic acid. RXRA serves as a common heterodimeric partner for a number of nuclear receptors. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation, chromatin condensation and transcriptional suppression. On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation. The RXRA/PPARA heterodimer is required for PPARA transcriptional activity on fatty acid oxidation genes such as ACOX1 and the P450 system genes.<ref>PMID:10195690</ref> <ref>PMID:11162439</ref> <ref>PMID:11915042</ref> <ref>PMID:20215566</ref> [[http://www.uniprot.org/uniprot/NCOA2_HUMAN NCOA2_HUMAN]] Transcriptional coactivator for steroid receptors and nuclear receptors. Coactivator of the steroid binding domain (AF-2) but not of the modulating N-terminal domain (AF-1). Required with NCOA1 to control energy balance between white and brown adipose tissues.<ref>PMID:9430642</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nuclear receptors (NRs) are conditional transcription factors with common multidomain organization that bind diverse DNA elements. How DNA sequences influence NR conformation is poorly understood. Here we report the crystal structure of the human retinoid X receptor alpha-liver X receptor beta (RXRalpha-LXRbeta) heterodimer on its cognate element, an AGGTCA direct repeat spaced by 4 nt. The complex has an extended X-shaped arrangement, with DNA- and ligand-binding domains crossed, in contrast to the parallel domain arrangement of other NRs that bind an AGGTCA direct repeat spaced by 1 nt. The LXRbeta core binds DNA via canonical contacts and auxiliary DNA contacts that enhance affinity for the response element. Comparisons of RXRalpha-LXRbetas in the crystal asymmetric unit and with previous NR structures reveal flexibility in NR organization and suggest a role for RXRalpha in adaptation of heterodimeric complexes to DNA.

-	~~==Function==~~	+	Structure of the retinoid X receptor alpha-liver X receptor beta (RXRalpha-LXRbeta) heterodimer on DNA.,Lou X, Toresson G, Benod C, Suh JH, Philips KJ, Webb P, Gustafsson JA Nat Struct Mol Biol. 2014 Mar;21(3):277-81. doi: 10.1038/nsmb.2778. Epub 2014 Feb, 23. PMID:24561505<ref>PMID:24561505</ref>
-	~~[[http://www.uniprot.org/uniprot/RXRA_HUMAN RXRA_HUMAN]] Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all~~-~~trans or 9~~-~~cis retinoic acid~~, ~~and regulate gene expression in various biological processes~~. ~~The RAR/RXR heterodimers bind to the retinoic acid response elements~~ (~~RARE~~) ~~composed of tandem 5'~~-~~AGGTCA-3' sites known as DR1-DR5~~. ~~The high affinity ligand for RXRs is 9-cis retinoic acid~~. ~~RXRA serves as a common heterodimeric partner for a number of nuclear receptors. The RXR~~/~~RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5~~. In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation, chromatin condensation and transcriptional suppression. ~~On ligand binding~~, ~~the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation~~. ~~The RXRA/PPARA heterodimer is required for PPARA transcriptional activity on fatty acid oxidation genes such as ACOX1 and the P450 system genes.<ref>~~PMID:10195690</ref> <ref>PMID:11162439</ref> <ref>PMID:11915042</ref> <ref>PMID:20215566</ref> [[http://www.uniprot.org/uniprot/NCOA2_HUMAN NCOA2_HUMAN]] Transcriptional coactivator for steroid receptors and nuclear receptors. Coactivator of the steroid binding domain (AF-2) but not of the modulating N-terminal domain (AF-1). Required with NCOA1 to control energy balance between white and brown adipose tissues.<ref>PMID:~~9430642~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4nqa]] is~~ a ~~12 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4NQA OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:024561505</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Retinoid X receptor\|Retinoid X receptor]]
-	[[Category: Benod, C.]]	+	== References ==
-	[[Category: Gustafsson, J A.]]	+	<references/>
-	[[Category: Lou, X H.]]	+	__TOC__
-	[[Category: Phillips, K J.]]	+	</StructureSection>
-	[[Category: Suh, J H.]]	+	[[Category: Human]]
-	[[Category: Toresson, G.]]	+	[[Category: Benod, C]]
-	[[Category: Webb, P.]]	+	[[Category: Gustafsson, J A]]
		+	[[Category: Lou, X H]]
		+	[[Category: Phillips, K J]]
		+	[[Category: Suh, J H]]
		+	[[Category: Toresson, G]]
		+	[[Category: Webb, P]]
	[[Category: Dbd]]		[[Category: Dbd]]
	[[Category: Lbd]]		[[Category: Lbd]]

OCA at 08:45, 19 March 2014

2014-03-19T08:45:00Z

←Older revision		Revision as of 08:45, 19 March 2014
Line 1:		Line 1:
	{{STRUCTURE_4nqa\| PDB=4nqa \| SCENE= }}		{{STRUCTURE_4nqa\| PDB=4nqa \| SCENE= }}
	===Crystal structure of liganded hRXR-alpha/hLXR-beta heterodimer on DNA===		===Crystal structure of liganded hRXR-alpha/hLXR-beta heterodimer on DNA===
		+	{{ABSTRACT_PUBMED_24561505}}

	==Disease==		==Disease==
Line 12:		Line 13:

	==Reference==		==Reference==
-	<references group="xtra"/><references/>	+	<ref group="xtra">PMID:024561505</ref><references group="xtra"/><references/>
	[[Category: Benod, C.]]		[[Category: Benod, C.]]
	[[Category: Gustafsson, J A.]]		[[Category: Gustafsson, J A.]]

OCA at 18:26, 3 March 2014

2014-03-03T18:26:49Z

←Older revision		Revision as of 18:26, 3 March 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4nqa\| PDB=4nqa \| SCENE= }}
		+	===Crystal structure of liganded hRXR-alpha/hLXR-beta heterodimer on DNA===

-	~~The entry 4nqa is ON HOLD until Paper Publication~~	+	==Disease==
		+	[[http://www.uniprot.org/uniprot/NCOA2_HUMAN NCOA2_HUMAN]] Note=Chromosomal aberrations involving NCOA2 may be a cause of acute myeloid leukemias. Inversion inv(8)(p11;q13) generates the KAT6A-NCOA2 oncogene, which consists of the N-terminal part of KAT6A and the C-terminal part of NCOA2/TIF2. KAT6A-NCOA2 binds to CREBBP and disrupts its function in transcription activation.

-	~~Authors~~: ~~Lou, X~~.H.~~, Gudrun, T~~., ~~Benod~~, C.~~, Suh, J~~.H.~~, Phillips, K~~., ~~Webb~~, P., ~~Gustafsson, J~~.A.	+	==Function==
		+	[[http://www.uniprot.org/uniprot/RXRA_HUMAN RXRA_HUMAN]] Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for RXRs is 9-cis retinoic acid. RXRA serves as a common heterodimeric partner for a number of nuclear receptors. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation, chromatin condensation and transcriptional suppression. On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation. The RXRA/PPARA heterodimer is required for PPARA transcriptional activity on fatty acid oxidation genes such as ACOX1 and the P450 system genes.<ref>PMID:10195690</ref> <ref>PMID:11162439</ref> <ref>PMID:11915042</ref> <ref>PMID:20215566</ref> [[http://www.uniprot.org/uniprot/NCOA2_HUMAN NCOA2_HUMAN]] Transcriptional coactivator for steroid receptors and nuclear receptors. Coactivator of the steroid binding domain (AF-2) but not of the modulating N-terminal domain (AF-1). Required with NCOA1 to control energy balance between white and brown adipose tissues.<ref>PMID:9430642</ref>

-	~~Description: Crystal~~ structure ~~of liganded hRXR~~-~~alpha~~/~~hLXR~~-~~beta heterodimer on DNA~~	+	==About this Structure==
		+	[[4nqa]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NQA OCA].
		+
		+	==Reference==
		+	<references group="xtra"/><references/>
		+	[[Category: Benod, C.]]
		+	[[Category: Gustafsson, J A.]]
		+	[[Category: Lou, X H.]]
		+	[[Category: Phillips, K J.]]
		+	[[Category: Suh, J H.]]
		+	[[Category: Toresson, G.]]
		+	[[Category: Webb, P.]]
		+	[[Category: Dbd]]
		+	[[Category: Lbd]]
		+	[[Category: Ligand]]
		+	[[Category: Lxr]]
		+	[[Category: Multi-domain]]
		+	[[Category: Rxr]]
		+	[[Category: Transcription regulator-dna complex]]
		+	[[Category: Zinc finger]]

OCA at 10:19, 5 February 2014

2014-02-05T10:19:17Z

←Older revision		Revision as of 10:19, 5 February 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4nqa is ON HOLD	+	The entry 4nqa is ON HOLD until Paper Publication

	Authors: Lou, X.H., Gudrun, T., Benod, C., Suh, J.H., Phillips, K., Webb, P., Gustafsson, J.A.		Authors: Lou, X.H., Gudrun, T., Benod, C., Suh, J.H., Phillips, K., Webb, P., Gustafsson, J.A.

	Description: Crystal structure of liganded hRXR-alpha/hLXR-beta heterodimer on DNA		Description: Crystal structure of liganded hRXR-alpha/hLXR-beta heterodimer on DNA

OCA at 09:26, 25 December 2013

2013-12-25T09:26:06Z

←Older revision		Revision as of 09:26, 25 December 2013
Line 5:		Line 5:
	Authors: Lou, X.H., Gudrun, T., Benod, C., Suh, J.H., Phillips, K., Webb, P., Gustafsson, J.A.		Authors: Lou, X.H., Gudrun, T., Benod, C., Suh, J.H., Phillips, K., Webb, P., Gustafsson, J.A.

-	Description: Crystal structure of liganded hRXR /hLXR heterodimer on DNA	+	Description: Crystal structure of liganded hRXR-alpha/hLXR-beta heterodimer on DNA