1kb4

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(New page: 200px<br /> <applet load="1kb4" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kb4, resolution 2.80&Aring;" /> '''Crystal Structure o...)
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[[Image:1kb4.gif|left|200px]]<br />
 
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<applet load="1kb4" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1kb4, resolution 2.80&Aring;" />
 
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'''Crystal Structure of VDR DNA-binding Domain Bound to a Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element'''<br />
 
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==Overview==
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==Crystal Structure of VDR DNA-binding Domain Bound to a Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element==
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The vitamin D receptor (VDR) forms homo- or heterodimers on response, elements composed of two hexameric half-sites separated by 3 bp of spacer, DNA. We describe here the crystal structures at 2.7-2.8 A resolution of, the VDR DNA-binding region (DBD) in complex with response elements from, three different promoters: osteopontin (SPP), canonical DR3 and, osteocalcin (OC). These structures reveal the chemical basis for the, increased affinity of VDR for the SPP response element, and for the poor, stability of the VDR-OC complex, relative to the canonical DR3 response, element. The homodimeric protein-protein interface is stabilized by van, der Waals interactions and is predominantly non-polar. An extensive, alpha-helix at the C-terminal end of the VDR DBD resembles that found in, the thyroid hormone receptor (TR), and suggests a mechanism by which VDR, and TR discriminate among response elements. Selective structure-based, mutations in the asymmetric homodimeric interface result in a VDR DBD, protein that is defective in homodimerization but now forms heterodimers, with the 9-cis retinoic acid receptor (RXR) DBD.
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<StructureSection load='1kb4' size='340' side='right'caption='[[1kb4]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1kb4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KB4 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kb4 OCA], [https://pdbe.org/1kb4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kb4 RCSB], [https://www.ebi.ac.uk/pdbsum/1kb4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kb4 ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN] Defects in VDR are the cause of rickets vitamin D-dependent type 2A (VDDR2A) [MIM:[https://omim.org/entry/277440 277440]. A disorder of vitamin D metabolism resulting in severe rickets, hypocalcemia and secondary hyperparathyroidism. Most patients have total alopecia in addition to rickets.<ref>PMID:2849209</ref> <ref>PMID:8381803</ref> <ref>PMID:1652893</ref> <ref>PMID:2177843</ref> <ref>PMID:8106618</ref> <ref>PMID:8392085</ref> <ref>PMID:7828346</ref> <ref>PMID:8675579</ref> <ref>PMID:8961271</ref> <ref>PMID:9005998</ref>
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== Function ==
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[https://www.uniprot.org/uniprot/VDR_HUMAN VDR_HUMAN] 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:16252006</ref> <ref>PMID:10678179</ref> <ref>PMID:15728261</ref> <ref>PMID:16913708</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kb/1kb4_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1kb4 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The vitamin D receptor (VDR) forms homo- or heterodimers on response elements composed of two hexameric half-sites separated by 3 bp of spacer DNA. We describe here the crystal structures at 2.7-2.8 A resolution of the VDR DNA-binding region (DBD) in complex with response elements from three different promoters: osteopontin (SPP), canonical DR3 and osteocalcin (OC). These structures reveal the chemical basis for the increased affinity of VDR for the SPP response element, and for the poor stability of the VDR-OC complex, relative to the canonical DR3 response element. The homodimeric protein-protein interface is stabilized by van der Waals interactions and is predominantly non-polar. An extensive alpha-helix at the C-terminal end of the VDR DBD resembles that found in the thyroid hormone receptor (TR), and suggests a mechanism by which VDR and TR discriminate among response elements. Selective structure-based mutations in the asymmetric homodimeric interface result in a VDR DBD protein that is defective in homodimerization but now forms heterodimers with the 9-cis retinoic acid receptor (RXR) DBD.
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==Disease==
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Structural basis of VDR-DNA interactions on direct repeat response elements.,Shaffer PL, Gewirth DT EMBO J. 2002 May 1;21(9):2242-52. PMID:11980721<ref>PMID:11980721</ref>
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Known diseases associated with this structure: Osteoporosis, involutional, 166710 (1) OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=601769 601769]], Rickets, vitamin D-resistant, type IIA OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=601769 601769]]
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1KB4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KB4 OCA].
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</div>
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<div class="pdbe-citations 1kb4" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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Structural basis of VDR-DNA interactions on direct repeat response elements., Shaffer PL, Gewirth DT, EMBO J. 2002 May 1;21(9):2242-52. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11980721 11980721]
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*[[Sandbox vdr|Sandbox vdr]]
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*[[Vitamin D receptor 3D structures|Vitamin D receptor 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Gewirth, D.T.]]
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[[Category: Gewirth DT]]
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[[Category: Shaffer, P.L.]]
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[[Category: Shaffer PL]]
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[[Category: ZN]]
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[[Category: nuclear receptor]]
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[[Category: protein-dna complex]]
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[[Category: vdr]]
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[[Category: vitamin d]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 17:49:29 2007''
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Current revision

Crystal Structure of VDR DNA-binding Domain Bound to a Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element

PDB ID 1kb4

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