3afr: Difference between revisions

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 ==Crystal Structure of VDR-LBD/22S-Butyl-1a,24R-dihydroxyvitamin D3 complex==
-<StructureSection load='3afr' size='340' side='right' caption='[[3afr]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='3afr' size='340' side='right'caption='[[3afr]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3afr]] 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=3AFR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AFR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3afr]] 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=3AFR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AFR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ICJ:(1R,3S,5Z)-5-[(2E)-2-{(1R,3AS,7AR)-1-[(1R,2S,4R)-2-BUTYL-4-HYDROXY-1,5-DIMETHYLHEXYL]-7A-METHYLOCTAHYDRO-4H-INDEN-4-YLIDENE}ETHYLIDENE]-4-METHYLIDENECYCLOHEXANE-1,3-DIOL'>ICJ</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&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2zxm|2zxm]], [[2zxn|2zxn]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ICJ:(1R,3S,5Z)-5-[(2E)-2-{(1R,3AS,7AR)-1-[(1R,2S,4R)-2-BUTYL-4-HYDROXY-1,5-DIMETHYLHEXYL]-7A-METHYLOCTAHYDRO-4H-INDEN-4-YLIDENE}ETHYLIDENE]-4-METHYLIDENECYCLOHEXANE-1,3-DIOL'>ICJ</scene></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 Rattus norvegicus])</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=3afr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3afr OCA], [https://pdbe.org/3afr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3afr RCSB], [https://www.ebi.ac.uk/pdbsum/3afr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3afr ProSAT]</span></td></tr>
-<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=3afr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3afr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3afr RCSB], [http://www.ebi.ac.uk/pdbsum/3afr PDBsum]</span></td></tr>
 </table>
 == 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_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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/af/3afr_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/af/3afr_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata 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=3afr ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3afr" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Sandbox vdr|Sandbox vdr]]
-*[[Vitamin D receptor|Vitamin D receptor]]
+*[[Vitamin D receptor 3D structures|Vitamin D receptor 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Rattus norvegicus]]
-[[Category: Ikura, T]]
+[[Category: Xenopus tropicalis]]
-[[Category: Inaba, Y]]
+[[Category: Ikura T]]
-[[Category: Ito, N]]
+[[Category: Inaba Y]]
-[[Category: Itoh, T]]
+[[Category: Ito N]]
-[[Category: Nakabayashi, M]]
+[[Category: Itoh T]]
-[[Category: Yamamoto, K]]
+[[Category: Nakabayashi M]]
-[[Category: Agonist]]
+[[Category: Yamamoto K]]
-[[Category: Antagonist]]
-[[Category: Dna-binding]]
-[[Category: Nuclear receptor]]
-[[Category: Nucleus]]
-[[Category: Receptor]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Transcription-transcription regulator complex]]
-[[Category: Vitamin d derivative]]
-[[Category: Vitamin d receptor]]