3w5r: Difference between revisions

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 ==Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives==
-<StructureSection load='3w5r' size='340' side='right' caption='[[3w5r]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='3w5r' size='340' side='right'caption='[[3w5r]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3w5r]] 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=3W5R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W5R FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3w5r]] 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=3W5R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W5R FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LOA:(3BETA,5BETA,9BETA)-3-(ACETYLOXY)CHOLAN-24-OIC+ACID'>LOA</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]] 2.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3w5p|3w5p]], [[3w5q|3w5q]], [[3w5t|3w5t]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LOA:(3BETA,5BETA,9BETA)-3-(ACETYLOXY)CHOLAN-24-OIC+ACID'>LOA</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 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=3w5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w5r OCA], [https://pdbe.org/3w5r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w5r RCSB], [https://www.ebi.ac.uk/pdbsum/3w5r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w5r 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=3w5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w5r OCA], [http://pdbe.org/3w5r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3w5r RCSB], [http://www.ebi.ac.uk/pdbsum/3w5r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3w5r ProSAT]</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_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;">
 == Publication Abstract from PubMed ==
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 </div>
 <div class="pdbe-citations 3w5r" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Sandbox vdr|Sandbox vdr]]
+*[[Vitamin D receptor 3D structures|Vitamin D receptor 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Buffalo rat]]
+[[Category: Homo sapiens]]
-[[Category: Ikura, T]]
+[[Category: Large Structures]]
-[[Category: Ito, N]]
+[[Category: Rattus norvegicus]]
-[[Category: Masuno, H]]
+[[Category: Ikura T]]
-[[Category: Activator]]
+[[Category: Ito N]]
-[[Category: Dna-binding]]
+[[Category: Masuno H]]
-[[Category: Metal-binding]]
-[[Category: Nuclear receptor-agonist complex]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Receptor]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Zinc-finger]]