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3cqv

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{{Seed}}
 
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[[Image:3cqv.png|left|200px]]
 
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<!--
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==Crystal structure of Reverb beta in complex with heme==
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The line below this paragraph, containing "STRUCTURE_3cqv", creates the "Structure Box" on the page.
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<StructureSection load='3cqv' size='340' side='right'caption='[[3cqv]], [[Resolution|resolution]] 1.90&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'>[[3cqv]] is a 1 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=3CQV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CQV FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
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-->
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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{{STRUCTURE_3cqv| PDB=3cqv | SCENE= }}
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NR1D2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
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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=3cqv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cqv OCA], [https://pdbe.org/3cqv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cqv RCSB], [https://www.ebi.ac.uk/pdbsum/3cqv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cqv ProSAT]</span></td></tr>
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</table>
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== Function ==
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[[https://www.uniprot.org/uniprot/NR1D2_HUMAN NR1D2_HUMAN]] Binds to the sequences 5'-AATGTAGGTCA-3' and 5'-ATAACTAGGTCA-3'. Acts as a potent competitive repressor of ROR alpha function (By similarity).
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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/cq/3cqv_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=3cqv 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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Heme is a ligand for the human nuclear receptors (NR) REV-ERBalpha and REV-ERBbeta, which are transcriptional repressors that play important roles in circadian rhythm, lipid and glucose metabolism, and diseases such as diabetes, atherosclerosis, inflammation, and cancer. Here we show that transcription repression mediated by heme-bound REV-ERBs is reversed by the addition of nitric oxide (NO), and that the heme and NO effects are mediated by the C-terminal ligand-binding domain (LBD). A 1.9 A crystal structure of the REV-ERBbeta LBD, in complex with the oxidized Fe(III) form of heme, shows that heme binds in a prototypical NR ligand-binding pocket, where the heme iron is coordinately bound by histidine 568 and cysteine 384. Under reducing conditions, spectroscopic studies of the heme-REV-ERBbeta complex reveal that the Fe(II) form of the LBD transitions between penta-coordinated and hexa-coordinated structural states, neither of which possess the Cys384 bond observed in the oxidized state. In addition, the Fe(II) LBD is also able to bind either NO or CO, revealing a total of at least six structural states of the protein. The binding of known co-repressors is shown to be highly dependent upon these various liganded states. REV-ERBs are thus highly dynamic receptors that are responsive not only to heme, but also to redox and gas. Taken together, these findings suggest new mechanisms for the systemic coordination of molecular clocks and metabolism. They also raise the possibility for gas-based therapies for the many disorders associated with REV-ERB biological functions.
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===Crystal structure of Reverb beta in complex with heme===
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The structural basis of gas-responsive transcription by the human nuclear hormone receptor REV-ERBbeta.,Pardee KI, Xu X, Reinking J, Schuetz A, Dong A, Liu S, Zhang R, Tiefenbach J, Lajoie G, Plotnikov AN, Botchkarev A, Krause HM, Edwards A PLoS Biol. 2009 Feb 24;7(2):e43. PMID:19243223<ref>PMID:19243223</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_19243223}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3cqv" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19243223 is the PubMed ID number.
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== References ==
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-->
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<references/>
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{{ABSTRACT_PUBMED_19243223}}
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__TOC__
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</StructureSection>
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==About this Structure==
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3CQV is a 1 chain 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=3CQV OCA].
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==Reference==
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<ref group="xtra">PMID:19243223</ref><references group="xtra"/>
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Arrowsmith, C H.]]
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[[Category: Large Structures]]
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[[Category: Botchkarev, A.]]
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[[Category: Arrowsmith, C H]]
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[[Category: Bountra, C.]]
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[[Category: Botchkarev, A]]
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[[Category: Cui, H.]]
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[[Category: Bountra, C]]
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[[Category: Dong, A.]]
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[[Category: Cui, H]]
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[[Category: Edwards, A.]]
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[[Category: Dong, A]]
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[[Category: Krause, H.]]
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[[Category: Edwards, A]]
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[[Category: Pardee, K I.]]
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[[Category: Krause, H]]
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[[Category: Reinking, J.]]
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[[Category: Pardee, K I]]
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[[Category: SGC, Structural Genomics Consortium.]]
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[[Category: Reinking, J]]
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[[Category: Savchenko, A.]]
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[[Category: Structural genomic]]
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[[Category: Schuetz, A.]]
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[[Category: Savchenko, A]]
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[[Category: Weigelt, J.]]
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[[Category: Schuetz, A]]
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[[Category: Xu, X.]]
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[[Category: Weigelt, J]]
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[[Category: Zhang, R.]]
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[[Category: Xu, X]]
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[[Category: Zhang, R]]
[[Category: Dna-binding]]
[[Category: Dna-binding]]
[[Category: Heme]]
[[Category: Heme]]
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[[Category: Reverb beta]]
[[Category: Reverb beta]]
[[Category: Sgc]]
[[Category: Sgc]]
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[[Category: Structural genomic]]
 
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[[Category: Structural genomics consortium]]
 
[[Category: Transcription]]
[[Category: Transcription]]
[[Category: Transcription regulation]]
[[Category: Transcription regulation]]
[[Category: Zinc]]
[[Category: Zinc]]
[[Category: Zinc-finger]]
[[Category: Zinc-finger]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 29 21:00:21 2009''
 

Current revision

Crystal structure of Reverb beta in complex with heme

PDB ID 3cqv

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