3vrw

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[[Image:3vrw.jpg|left|200px]]
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==VDR ligand binding domain in complex with 22S-Butyl-2-methylidene-26,27-dimethyl-19,24-dinor-1alpha,25-dihydroxyvitamin D3==
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<StructureSection load='3vrw' size='340' side='right' caption='[[3vrw]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3vrw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VRW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VRW FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YS5:(1R,3R,7E,17BETA)-17-[(2R,3S)-3-BUTYL-5-ETHYL-5-HYDROXYHEPTAN-2-YL]-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>YS5</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3vrt|3vrt]], [[3vru|3vru]], [[3vrv|3vrv]]</td></tr>
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<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 Rattus norvegicus])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vrw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vrw RCSB], [http://www.ebi.ac.uk/pdbsum/3vrw PDBsum]</span></td></tr>
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</table>
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== Function ==
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[[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>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Previously, we reported that 22S-butyl-25,26,27-trinor-1alpha,24-dihydroxyvitamin D(3)2 represents a new class of antagonist for the vitamin D receptor (VDR). The crystal structure of the ligand-binding domain (LBD) of VDR complexed with 2 showed the formation of a butyl pocket to accommodate the 22-butyl group and insufficient interactions between ligand 2 and the C-terminus of VDR. Here, we designed and synthesized new analogues 5a-c and evaluated their biological activities to probe whether agonistic activity is recovered when the analogue restores interactions with the C-terminus of VDR. Analogues 5a-c exhibited full agonistic activity in transactivation. Interestingly, 5c, which bears a 24-diethyl group, completely recovered agonistic activity, although 3c and 4c act as an antagonist and a weak agonist, respectively. The crystal structures of VDR-LBD complexed with 3a, 4a, 5a, and 5c were solved, and the results confirmed that butyl pocket formation in VDR strongly affects the agonistic or antagonistic behaviors of ligands.
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Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands.,Yoshimoto N, Sakamaki Y, Haeta M, Kato A, Inaba Y, Itoh T, Nakabayashi M, Ito N, Yamamoto K J Med Chem. 2012 May 10;55(9):4373-81. Epub 2012 Apr 27. PMID:22512505<ref>PMID:22512505</ref>
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The line below this paragraph, containing "STRUCTURE_3vrw", creates the "Structure Box" on the page.
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{{STRUCTURE_3vrw| PDB=3vrw | SCENE= }}
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===VDR ligand binding domain in complex with 22S-Butyl-2-methylidene-26,27-dimethyl-19,24-dinor-1alpha,25-dihydroxyvitamin D3===
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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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==See Also==
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<!--
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*[[Sandbox vdr|Sandbox vdr]]
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The line below this paragraph, {{ABSTRACT_PUBMED_22512505}}, adds the Publication Abstract to the page
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*[[Vitamin D receptor|Vitamin D receptor]]
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(as it appears on PubMed at http://www.pubmed.gov), where 22512505 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_22512505}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[3vrw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VRW OCA].
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==Reference==
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<ref group="xtra">PMID:022512505</ref><references group="xtra"/>
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[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
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[[Category: Inaba, Y.]]
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[[Category: Inaba, Y]]
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[[Category: Ito, N.]]
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[[Category: Ito, N]]
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[[Category: Itoh, T.]]
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[[Category: Itoh, T]]
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[[Category: Nakabayashi, M.]]
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[[Category: Nakabayashi, M]]
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[[Category: Yamamoto, K.]]
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[[Category: Yamamoto, K]]
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[[Category: Yoshimoto, N.]]
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[[Category: Yoshimoto, N]]
[[Category: Co-factor]]
[[Category: Co-factor]]
[[Category: Nuclear]]
[[Category: Nuclear]]

Revision as of 13:09, 25 December 2014

VDR ligand binding domain in complex with 22S-Butyl-2-methylidene-26,27-dimethyl-19,24-dinor-1alpha,25-dihydroxyvitamin D3

3vrw, resolution 2.40Å

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