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<StructureSection load='2zmi' size='340' side='right'caption='[[2zmi]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
<StructureSection load='2zmi' size='340' side='right'caption='[[2zmi]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2zmi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZMI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZMI FirstGlance]. <br>
<table><tr><td colspan='2'>[[2zmi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] and [https://en.wikipedia.org/wiki/Xenopus_tropicalis Xenopus tropicalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZMI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZMI FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=TT2:(1R,3R,7E,17BETA)-17-{(1S,2E,5R)-5-HYDROXY-1-METHYL-5-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]PENT-2-EN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>TT2</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]] 1.7&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2zmh|2zmh]], [[2zmj|2zmj]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=TT2:(1R,3R,7E,17BETA)-17-{(1S,2E,5R)-5-HYDROXY-1-METHYL-5-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]PENT-2-EN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>TT2</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Vdr, Nr1i1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=2zmi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zmi OCA], [https://pdbe.org/2zmi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zmi RCSB], [https://www.ebi.ac.uk/pdbsum/2zmi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zmi 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=2zmi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zmi OCA], [https://pdbe.org/2zmi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zmi RCSB], [https://www.ebi.ac.uk/pdbsum/2zmi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zmi ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[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> [[https://www.uniprot.org/uniprot/MED1_XENTR MED1_XENTR]] 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 (By similarity).
[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>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=2zmi 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=2zmi ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The X-ray crystal structures of the rat VDR ligand-binding domain complexed with 19-norvitamin D compounds that contain an adamantyl substituent at the side-chain terminus, 2a (ADTT), 2b (ADNY), and 2c (ADMI4) and a coactivator peptide derived from DRIP205 are reported. These compounds show a series of partial agonistic (10-75% efficacy)/antagonistic activities. All of these complexed receptors are crystallized in the canonical active conformation, regardless of their activity profiles. The bulky adamantyl side chain does not crowd helix 12 but protrudes into the gap formed by helix 11, loop 11-12, helix 3, and loop 6-7, thereby widening the ligand binding pocket. We suggest that these structural changes destabilize the active protein conformation and reduce its contribution to equilibrium among the active and inactive conformations. The coactivator peptide traps the minor active conformation, and the equilibrium shifts to the active conformation. As a result, these ligands show partial agonistic activities.
Crystal Structures of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and Partial Agonism.,Nakabayashi M, Yamada S, Yoshimoto N, Tanaka T, Igarashi M, Ikura T, Ito N, Makishima M, Tokiwa H, Deluca HF, Shimizu M J Med Chem. 2008 Aug 19. PMID:18710208<ref>PMID:18710208</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2zmi" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Buffalo rat]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: DeLuca, H F]]
[[Category: Rattus norvegicus]]
[[Category: Igarashi, M]]
[[Category: Xenopus tropicalis]]
[[Category: Ikura, T]]
[[Category: DeLuca HF]]
[[Category: Ito, N]]
[[Category: Igarashi M]]
[[Category: Makishima, M]]
[[Category: Ikura T]]
[[Category: Nakabayashi, M]]
[[Category: Ito N]]
[[Category: Shimizu, M]]
[[Category: Makishima M]]
[[Category: Tanaka, T]]
[[Category: Nakabayashi M]]
[[Category: Tokiwa, H]]
[[Category: Shimizu M]]
[[Category: Yamada, S]]
[[Category: Tanaka T]]
[[Category: Yoshimoto, N]]
[[Category: Tokiwa H]]
[[Category: Activator]]
[[Category: Yamada S]]
[[Category: Dna-binding]]
[[Category: Yoshimoto N]]
[[Category: Metal-binding]]
[[Category: Nuclear receptor-antagonist complex]]
[[Category: Nucleus]]
[[Category: Phosphoprotein]]
[[Category: Receptor]]
[[Category: Transcription]]
[[Category: Transcription regulation]]
[[Category: Zinc]]
[[Category: Zinc-finger]]

Latest revision as of 13:57, 13 March 2024

Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism

2zmi, resolution 1.70Å

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