1by4

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[[Image:1by4.gif|left|200px]]
 
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==STRUCTURE AND MECHANISM OF THE HOMODIMERIC ASSEMBLY OF THE RXR ON DNA==
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The line below this paragraph, containing "STRUCTURE_1by4", creates the "Structure Box" on the page.
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<StructureSection load='1by4' size='340' side='right'caption='[[1by4]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1by4]] is a 8 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=1BY4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BY4 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_1by4| PDB=1by4 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1by4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1by4 OCA], [https://pdbe.org/1by4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1by4 RCSB], [https://www.ebi.ac.uk/pdbsum/1by4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1by4 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/by/1by4_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1by4 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The 9-cis retinoic acid receptor, RXR, binds DNA effectively as a homodimer or as a heterodimer with other nuclear receptors. The DNA-binding sites for these RXR complexes are direct repeats of a consensus sequence separated by one to five base-pairs of intervening space. Here, we report the 2.1 A crystal structure of the RXR-DNA-binding domain as a homodimer in complex with its idealized direct repeat DNA target. The structure shows how a gene-regulatory site can induce conformational changes in a transcription factor that promote homo-cooperative assembly. Specifically, an alpha-helix in the T-box is disrupted to allow efficient DNA-binding and subunit dimerization. RXR displays a relaxed mode of sequence recognition, interacting with only three base-pairs in each hexameric half-site. The structure illustrates how site selection is achieved in this large eukaryotic transcription factor family through discrete protein-protein interactions and the use of tandem DNA binding sites with characteristic spacings.
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'''STRUCTURE AND MECHANISM OF THE HOMODIMERIC ASSEMBLY OF THE RXR ON DNA'''
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Structural basis of RXR-DNA interactions.,Zhao Q, Chasse SA, Devarakonda S, Sierk ML, Ahvazi B, Rastinejad F J Mol Biol. 2000 Feb 18;296(2):509-20. PMID:10669605<ref>PMID:10669605</ref>
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==Overview==
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The 9-cis retinoic acid receptor, RXR, binds DNA effectively as a homodimer or as a heterodimer with other nuclear receptors. The DNA-binding sites for these RXR complexes are direct repeats of a consensus sequence separated by one to five base-pairs of intervening space. Here, we report the 2.1 A crystal structure of the RXR-DNA-binding domain as a homodimer in complex with its idealized direct repeat DNA target. The structure shows how a gene-regulatory site can induce conformational changes in a transcription factor that promote homo-cooperative assembly. Specifically, an alpha-helix in the T-box is disrupted to allow efficient DNA-binding and subunit dimerization. RXR displays a relaxed mode of sequence recognition, interacting with only three base-pairs in each hexameric half-site. The structure illustrates how site selection is achieved in this large eukaryotic transcription factor family through discrete protein-protein interactions and the use of tandem DNA binding sites with characteristic spacings.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1BY4 is a [[Single protein]] structure of 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=1BY4 OCA].
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</div>
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<div class="pdbe-citations 1by4" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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Structural basis of RXR-DNA interactions., Zhao Q, Chasse SA, Devarakonda S, Sierk ML, Ahvazi B, Rastinejad F, J Mol Biol. 2000 Feb 18;296(2):509-20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10669605 10669605]
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*[[Retinoid X receptor 3D structures|Retinoid X receptor 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Ahvazi, B.]]
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[[Category: Ahvazi B]]
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[[Category: Chasse, S A.]]
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[[Category: Chasse SA]]
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[[Category: Devarakonda, S.]]
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[[Category: Devarakonda S]]
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[[Category: Rastinejad, F.]]
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[[Category: Rastinejad F]]
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[[Category: Sierk, M L.]]
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[[Category: Sierk ML]]
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[[Category: Sigler, P B.]]
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[[Category: Sigler PB]]
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[[Category: Zhao, Q.]]
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[[Category: Zhao Q]]
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[[Category: Crystal structure]]
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[[Category: Hormone response element]]
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[[Category: Nuclear receptor]]
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[[Category: Protein-dna interation]]
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[[Category: Rxr]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 12:06:18 2008''
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Current revision

STRUCTURE AND MECHANISM OF THE HOMODIMERIC ASSEMBLY OF THE RXR ON DNA

PDB ID 1by4

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