1xdk: Difference between revisions

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 ==Crystal Structure of the RARbeta/RXRalpha Ligand Binding Domain Heterodimer in Complex with 9-cis Retinoic Acid and a Fragment of the TRAP220 Coactivator==
-<StructureSection load='1xdk' size='340' side='right' caption='[[1xdk]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='1xdk' size='340' side='right'caption='[[1xdk]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1xdk]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XDK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1xdk]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XDK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=REA:RETINOIC+ACID'>REA</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dkf|1dkf]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9CR:(9CIS)-RETINOIC+ACID'>9CR</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=10090 LK3 transgenic mice]), Rarb, Nr1b2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=1xdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdk OCA], [https://pdbe.org/1xdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xdk RCSB], [https://www.ebi.ac.uk/pdbsum/1xdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xdk 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=1xdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdk OCA], [http://pdbe.org/1xdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xdk RCSB], [http://www.ebi.ac.uk/pdbsum/1xdk PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RXRA_MOUSE RXRA_MOUSE]] 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:1310259</ref> <ref>PMID:10383391</ref> <ref>PMID:12032153</ref>  [[http://www.uniprot.org/uniprot/MED1_MOUSE MED1_MOUSE]] 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. Essential for embryogenesis, including development of the central nervous system, heart, liver and placenta and for erythropoiesis. Also required for normal transcriptional control of thyroid-stimulating hormone beta (TSHB) in the pituitary.<ref>PMID:9325263</ref> <ref>PMID:14500757</ref> <ref>PMID:10882104</ref> <ref>PMID:12037571</ref> <ref>PMID:11867769</ref> <ref>PMID:14636573</ref> <ref>PMID:15150259</ref> <ref>PMID:15340084</ref> <ref>PMID:16137621</ref> <ref>PMID:17132730</ref>  [[http://www.uniprot.org/uniprot/RARB_MOUSE RARB_MOUSE]] 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. In the absence of ligand, acts mainly as an activator of gene expression due to weak binding to corepressors (By similarity). In concert with RARG, required for skeletal growth, matrix homeostasis and growth plate function.
+[https://www.uniprot.org/uniprot/RXRA_MOUSE RXRA_MOUSE] 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:1310259</ref> <ref>PMID:10383391</ref> <ref>PMID:12032153</ref>
 == 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/xd/1xdk_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xd/1xdk_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].
+</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=1xdk ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[Retinoic acid receptor|Retinoic acid receptor]]
+*[[Retinoic acid receptor 3D structures|Retinoic acid receptor 3D structures]]
-*[[Retinoid X receptor|Retinoid X receptor]]
+*[[Retinoid X receptor 3D structures|Retinoid X receptor 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Lk3 transgenic mice]]
+[[Category: Large Structures]]
-[[Category: Bourguet, W]]
+[[Category: Mus musculus]]
-[[Category: Germain, P]]
+[[Category: Bourguet W]]
-[[Category: Gronemeyer, H]]
+[[Category: De Lera AR]]
-[[Category: Guichou, J F]]
+[[Category: Germain P]]
-[[Category: Kammerer, S]]
+[[Category: Gronemeyer H]]
-[[Category: Lera, A R.De]]
+[[Category: Guichou JF]]
-[[Category: Perez, E]]
+[[Category: Kammerer S]]
-[[Category: Pogenberg, V]]
+[[Category: Perez E]]
-[[Category: Royer, C A]]
+[[Category: Pogenberg V]]
-[[Category: Vivat-Hannah, V]]
+[[Category: Royer CA]]
-[[Category: Coactivator]]
+[[Category: Vivat-Hannah V]]
-[[Category: Hormone-growth factor receptor complex]]
-[[Category: Ligand]]
-[[Category: Nuclear receptor]]