1rkh: Difference between revisions

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-{{Seed}}
-[[Image:1rkh.png|left|200px]]
-<!--
+==crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2AM20R and a synthetic peptide containing the NR2 box of DRIP 205==
-The line below this paragraph, containing "STRUCTURE_1rkh", creates the "Structure Box" on the page.
+<StructureSection load='1rkh' size='340' side='right'caption='[[1rkh]], [[Resolution|resolution]] 2.28&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1rkh]] 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=1RKH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RKH FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.28&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VD2:5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYL-CYCLOHEXANE-1,3-DIOL'>VD2</scene></td></tr>
-{{STRUCTURE_1rkh|  PDB=1rkh  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkh OCA], [https://pdbe.org/1rkh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rkh RCSB], [https://www.ebi.ac.uk/pdbsum/1rkh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rkh ProSAT]</span></td></tr>
+</table>
+== 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>
+== 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/rk/1rkh_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/main_output.php?pdb_ID=1rkh ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We have determined the crystal structures of the ligand binding domain (LBD) of the rat vitamin D receptor in ternary complexes with a synthetic LXXLL-containing peptide and the following four ligands: 1alpha,25-dihydroxyvitamin D(3); 2-methylene-19-nor-(20S)-1alpha,25-dihydroxyvitamin D(3) (2MD); 1alpha-hydroxy-2-methylene-19-nor-(20S)-bishomopregnacalciferol (2MbisP), and 2alpha-methyl-19-nor-1alpha,25-dihydroxyvitamin D(3) (2AM20R). The conformation of the LBD is identical in each complex. Binding of the 2-carbon-modified analogues does not change the positions of the amino acids in the ligand binding site and has no effect on the interactions in the coactivator binding pocket. The CD ring of the superpotent analogue, 2MD, is tilted within the binding site relative to the other ligands in this study and to (20S)-1alpha,25-dihydroxyvitamin D(3) [Tocchini-Valentini et al. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 5491-5496]. The aliphatic side chain of 2MD follows a different path within the binding site; nevertheless, the 25-hydroxyl group at the end of the chain occupies the same position as that of the natural ligand, and the hydrogen bonds with histidines 301 and 393 are maintained. 2MbisP binds to the receptor despite the absence of the 25-hydroxyl group. A water molecule is observed between His 301 and His 393 in this structure, and it preserves the orientation of the histidines in the binding site. Although the alpha-chair conformer is highly favored in solution for the A ring of 2AM20R, the crystal structures demonstrate that this ring assumes the beta-chair conformation in all cases, and the 1alpha-hydroxyl group is equatorial. The peptide folds as a helix and is anchored through hydrogen bonds to a surface groove formed by helices 3, 4, and 12. Electrostatic and hydrophobic interactions between the peptide and the LBD stabilize the active receptor conformation. This stablization appears necessary for crystal growth.
-===crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2AM20R and a synthetic peptide containing the NR2 box of DRIP 205===
+Molecular structure of the rat vitamin D receptor ligand binding domain complexed with 2-carbon-substituted vitamin D3 hormone analogues and a LXXLL-containing coactivator peptide.,Vanhooke JL, Benning MM, Bauer CB, Pike JW, DeLuca HF Biochemistry. 2004 Apr 13;43(14):4101-10. PMID:15065852<ref>PMID:15065852</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1rkh" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15065852}}, adds the Publication Abstract to the page
+*[[Sandbox vdr|Sandbox vdr]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15065852 is the PubMed ID number.
+*[[Vitamin D receptor 3D structures|Vitamin D receptor 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_15065852}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-RKH is a [[Protein complex]] structure of sequences 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=1RKH OCA].
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
-==Reference==
-Molecular structure of the rat vitamin D receptor ligand binding domain complexed with 2-carbon-substituted vitamin D3 hormone analogues and a LXXLL-containing coactivator peptide., Vanhooke JL, Benning MM, Bauer CB, Pike JW, DeLuca HF, Biochemistry. 2004 Apr 13;43(14):4101-10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15065852 15065852]
-[[Category: Protein complex]]
 [[Category: Rattus norvegicus]]
-[[Category: Bauer, C B.]]
+[[Category: Bauer CB]]
-[[Category: Benning, M M.]]
+[[Category: Benning MM]]
-[[Category: DeLuca, H F.]]
+[[Category: F DeLuca H]]
-[[Category: Pike, J W.]]
+[[Category: Pike JW]]
-[[Category: Vanhooke, J L.]]
+[[Category: Vanhooke JL]]
-[[Category: Nuclear receptor-coactivator interaction]]
-[[Category: Nuclear receptor-ligand complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 23:14:31 2008''