5yt2: Difference between revisions

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-'''Unreleased structure'''
-The entry 5yt2 is ON HOLD
+==Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R)-5-[(E)-2-{(1R,3aS,7aR)-1-[(R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-2,3,3a,6,7,7a-hexahydro-1H-inden-4-yl}vinyl]-2-(3-hydroxypropyl)cyclohex-4-ene-1,3-diol==
+<StructureSection load='5yt2' size='340' side='right'caption='[[5yt2]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5yt2]] 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=5YT2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YT2 FirstGlance]. <br>
+</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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=90O:(1R,2S,3R)-5-[(E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-1,2,3,3a,6,7-hexahydroinden-4-yl]ethenyl]-2-(3-oxidanylpropyl)cyclohex-4-ene-1,3-diol'>90O</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=5yt2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yt2 OCA], [https://pdbe.org/5yt2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yt2 RCSB], [https://www.ebi.ac.uk/pdbsum/5yt2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yt2 ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN] Defects in VDR are the cause of rickets vitamin D-dependent type 2A (VDDR2A) [MIM:[https://omim.org/entry/277440 277440]. A disorder of vitamin D metabolism resulting in severe rickets, hypocalcemia and secondary hyperparathyroidism. Most patients have total alopecia in addition to rickets.<ref>PMID:2849209</ref> <ref>PMID:8381803</ref> <ref>PMID:1652893</ref> <ref>PMID:2177843</ref> <ref>PMID:8106618</ref> <ref>PMID:8392085</ref> <ref>PMID:7828346</ref> <ref>PMID:8675579</ref> <ref>PMID:8961271</ref> <ref>PMID:9005998</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN] 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:16252006</ref> <ref>PMID:10678179</ref> <ref>PMID:15728261</ref> <ref>PMID:16913708</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Both 2alpha- and 2beta-hydroxypropyl substituted 14-epi-1alpha,25-dihydroxy-19-nortachysterols were synthesized to study the human vitamin D receptor (hVDR) binding affinity, binding configurations, and interactions with amino acid residues in the ligand binding domain of hVDR by X-ray co-crystallographic analysis. In conjunction with our previous results on 14-epi-19-nortachysterol, 2-methylidene-, 2alpha-methyl-, 2beta-methyl, and 2alpha-hydroxypropoxy-14-epi-19-nortachysterol, we propose a variety of effects of substitution at the C2 position in the 14-epi-19-nortachysterol skeleton on biological activities.
-Authors: Takimoto-Kamimura, M., Kakuda, S.
+Effects of 2-substitution on 14-epi-19-nortachysterol-mediated biological events: based on synthesis and X-ray co-crystallographic analysis with the human vitamin D receptor.,Sawada D, Kakuda S, Takeuchi A, Kawagoe F, Takimoto-Kamimura M, Kittaka A Org Biomol Chem. 2018 Apr 4;16(14):2448-2455. doi: 10.1039/C8OB00158H. PMID:29560490<ref>PMID:29560490</ref>
-Description: Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R)-5-[(E)-2-{(1R,3aS,7aR)-1-[(R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-2,3,3a,6,7,7a-hexahydro-1H-inden-4-yl}vinyl]-2-(3-hydroxypropyl)cyclohex-4-ene-1,3-diol
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Takimoto-Kamimura, M]]
+<div class="pdbe-citations 5yt2" style="background-color:#fffaf0;"></div>
-[[Category: Kakuda, S]]
+==See Also==
+*[[Vitamin D receptor 3D structures|Vitamin D receptor 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Kakuda S]]
+[[Category: Takimoto-Kamimura M]]