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| | <StructureSection load='6jez' size='340' side='right'caption='[[6jez]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='6jez' size='340' side='right'caption='[[6jez]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6jez]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JEZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JEZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6jez]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JEZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JEZ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EJO:7-(diethylamino)chromen-2-one'>EJO</scene>, <scene name='pdbligand=YSV:(1R,3R)-5-(2-((1R,3AS,7AR,E)-1-((R)-6-HYDROXY-6-METHYLHEPTAN-2-YL)-7A-METHYLOCTAHYDRO-4H-INDEN-4-YLIDENE)ETHYLIDENE)-2-METHYLENECYCLOHEXANE-1,3-DIOL'>YSV</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]] 2.3Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Vdr, Nr1i1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EJO:7-(diethylamino)chromen-2-one'>EJO</scene>, <scene name='pdbligand=YSV:(1R,3R)-5-(2-((1R,3AS,7AR,E)-1-((R)-6-HYDROXY-6-METHYLHEPTAN-2-YL)-7A-METHYLOCTAHYDRO-4H-INDEN-4-YLIDENE)ETHYLIDENE)-2-METHYLENECYCLOHEXANE-1,3-DIOL'>YSV</scene></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=6jez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jez OCA], [http://pdbe.org/6jez PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jez RCSB], [http://www.ebi.ac.uk/pdbsum/6jez PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jez 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=6jez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jez OCA], [https://pdbe.org/6jez PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jez RCSB], [https://www.ebi.ac.uk/pdbsum/6jez PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jez ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/VDR_RAT VDR_RAT]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:17227670</ref> [[http://www.uniprot.org/uniprot/MED1_HUMAN MED1_HUMAN]] 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.<ref>PMID:9653119</ref> <ref>PMID:10406464</ref> <ref>PMID:12218053</ref> <ref>PMID:12037571</ref> <ref>PMID:11867769</ref> <ref>PMID:12556447</ref> <ref>PMID:14636573</ref> <ref>PMID:15471764</ref> <ref>PMID:15340084</ref> <ref>PMID:15989967</ref> <ref>PMID:16574658</ref> | + | [https://www.uniprot.org/uniprot/VDR_RAT VDR_RAT] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:17227670</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Buffalo rat]] | + | [[Category: Homo sapiens]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Itoh, T]] | + | [[Category: Rattus norvegicus]] |
| - | [[Category: Kojima, H]] | + | [[Category: Itoh T]] |
| - | [[Category: Yamamoto, K]] | + | [[Category: Kojima H]] |
| - | [[Category: Covalent labeling]] | + | [[Category: Yamamoto K]] |
| - | [[Category: Histidine]]
| + | |
| - | [[Category: Hormone]]
| + | |
| - | [[Category: Tcc probe]]
| + | |
| - | [[Category: Turn-on fluorescent probe]]
| + | |
| Structural highlights
Function
VDR_RAT Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.[1]
Publication Abstract from PubMed
Fluorescent molecules have contributed to basic biological research but there are currently only a limited number of probes available for the detection of non-enzymatic proteins. Here, we report turn-on fluorescent probes mediated by conjugate addition and cyclization (TCC probes). These probes react with multiple amino acids and exhibit a 36-fold greater emission intensity after reaction. We analyzed the reactions between TCC probes and nuclear receptors by electrospray ionization mass spectrometry, X-ray crystallography, spectrofluorometry, and fluorescence microscopy. In vitro analysis showed that probes consisting of a protein ligand and TCC could label vitamin D receptor and peroxisome proliferator-activated receptor gamma. Moreover, we demonstrated that not only a ligand unit but also a peptide unit can label the target protein in a complex mixture.
Cyclization Reaction-Based Turn-on Probe for Covalent Labeling of Target Proteins.,Kojima H, Fujita Y, Takeuchi R, Ikebe Y, Ohashi N, Yamamoto K, Itoh T Cell Chem Biol. 2020 Jan 22. pii: S2451-9456(20)30006-4. doi:, 10.1016/j.chembiol.2020.01.006. PMID:31991094[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Vanhooke JL, Tadi BP, Benning MM, Plum LA, DeLuca HF. New analogs of 2-methylene-19-nor-(20S)-1,25-dihydroxyvitamin D3 with conformationally restricted side chains: evaluation of biological activity and structural determination of VDR-bound conformations. Arch Biochem Biophys. 2007 Apr 15;460(2):161-5. Epub 2006 Dec 12. PMID:17227670 doi:10.1016/j.abb.2006.11.029
- ↑ Kojima H, Fujita Y, Takeuchi R, Ikebe Y, Ohashi N, Yamamoto K, Itoh T. Cyclization Reaction-Based Turn-on Probe for Covalent Labeling of Target Proteins. Cell Chem Biol. 2020 Jan 22. pii: S2451-9456(20)30006-4. doi:, 10.1016/j.chembiol.2020.01.006. PMID:31991094 doi:http://dx.doi.org/10.1016/j.chembiol.2020.01.006
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