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[[Image:2hbh.jpg|left|200px]]
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{{STRUCTURE_2hbh|  PDB=2hbh  |  SCENE=  }}
'''Crystal structure of Vitamin D nuclear receptor ligand binding domain bound to a locked side-chain analog of calcitriol and SRC-1 peptide'''


==Crystal structure of Vitamin D nuclear receptor ligand binding domain bound to a locked side-chain analog of calcitriol and SRC-1 peptide==
<StructureSection load='2hbh' size='340' side='right'caption='[[2hbh]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2hbh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HBH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HBH FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.65&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XE4:1,3-CYCLOHEXANEDIOL,+4-METHYLENE-5-[(2E)-[(1S,3AS,7AS)-OCTAHYDRO-1-(5-HYDROXY-5-METHYL-1,3-HEXADIYNYL)-7A-METHYL-4H-INDEN-4-YLIDENE]ETHYLIDENE]-,+(1R,3S,5Z)'>XE4</scene></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=2hbh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hbh OCA], [https://pdbe.org/2hbh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hbh RCSB], [https://www.ebi.ac.uk/pdbsum/2hbh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hbh ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/VDRA_DANRE VDRA_DANRE] 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. Plays a central role in calcium homeostasis.<ref>PMID:17218092</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/hb/2hbh_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=2hbh ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structures of vitamin D nuclear receptor (VDR) have revealed that all compounds are anchored by the same residues to the ligand binding pocket (LBP). Based on this observation, a synthetic analog with a locked side chain (21-nor-calcitriol-20(22),23-diyne) has been synthesized in order to gain in entropy energy with a predefined active side chain conformation. The crystal structure of VDR LBD bound to this locked side chain analogue while confirming the docking provides a structural basis for the activity of this compound.


==Overview==
Crystal structure of the vitamin D nuclear receptor ligand binding domain in complex with a locked side chain analog of calcitriol.,Rochel N, Hourai S, Perez-Garcia X, Rumbo A, Mourino A, Moras D Arch Biochem Biophys. 2007 Apr 15;460(2):172-6. Epub 2007 Feb 20. PMID:17346665<ref>PMID:17346665</ref>
The crystal structures of vitamin D nuclear receptor (VDR) have revealed that all compounds are anchored by the same residues to the ligand binding pocket (LBP). Based on this observation, a synthetic analog with a locked side chain (21-nor-calcitriol-20(22),23-diyne) has been synthesized in order to gain in entropy energy with a predefined active side chain conformation. The crystal structure of VDR LBD bound to this locked side chain analogue while confirming the docking provides a structural basis for the activity of this compound.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
2HBH is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HBH OCA].
</div>
<div class="pdbe-citations 2hbh" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Crystal structure of the vitamin D nuclear receptor ligand binding domain in complex with a locked side chain analog of calcitriol., Rochel N, Hourai S, Perez-Garcia X, Rumbo A, Mourino A, Moras D, Arch Biochem Biophys. 2007 Apr 15;460(2):172-6. Epub 2007 Feb 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17346665 17346665]
*[[Sandbox vdr|Sandbox vdr]]
*[[Vitamin D receptor 3D structures|Vitamin D receptor 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Danio rerio]]
[[Category: Danio rerio]]
[[Category: Protein complex]]
[[Category: Homo sapiens]]
[[Category: Hourai, S.]]
[[Category: Large Structures]]
[[Category: Moras, D.]]
[[Category: Hourai S]]
[[Category: Rochel, N.]]
[[Category: Moras D]]
[[Category: Alpha helical sandwich]]
[[Category: Rochel N]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 06:05:28 2008''

Latest revision as of 11:50, 25 October 2023

Crystal structure of Vitamin D nuclear receptor ligand binding domain bound to a locked side-chain analog of calcitriol and SRC-1 peptideCrystal structure of Vitamin D nuclear receptor ligand binding domain bound to a locked side-chain analog of calcitriol and SRC-1 peptide

Structural highlights

2hbh is a 2 chain structure with sequence from Danio rerio and Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.65Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VDRA_DANRE 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. Plays a central role in calcium homeostasis.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The crystal structures of vitamin D nuclear receptor (VDR) have revealed that all compounds are anchored by the same residues to the ligand binding pocket (LBP). Based on this observation, a synthetic analog with a locked side chain (21-nor-calcitriol-20(22),23-diyne) has been synthesized in order to gain in entropy energy with a predefined active side chain conformation. The crystal structure of VDR LBD bound to this locked side chain analogue while confirming the docking provides a structural basis for the activity of this compound.

Crystal structure of the vitamin D nuclear receptor ligand binding domain in complex with a locked side chain analog of calcitriol.,Rochel N, Hourai S, Perez-Garcia X, Rumbo A, Mourino A, Moras D Arch Biochem Biophys. 2007 Apr 15;460(2):172-6. Epub 2007 Feb 20. PMID:17346665[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Ciesielski F, Rochel N, Moras D. Adaptability of the Vitamin D nuclear receptor to the synthetic ligand Gemini: remodelling the LBP with one side chain rotation. J Steroid Biochem Mol Biol. 2007 Mar;103(3-5):235-42. Epub 2007 Jan 10. PMID:17218092 doi:http://dx.doi.org/10.1016/j.jsbmb.2006.12.003
  2. ↑ Rochel N, Hourai S, Perez-Garcia X, Rumbo A, Mourino A, Moras D. Crystal structure of the vitamin D nuclear receptor ligand binding domain in complex with a locked side chain analog of calcitriol. Arch Biochem Biophys. 2007 Apr 15;460(2):172-6. Epub 2007 Feb 20. PMID:17346665 doi:10.1016/j.abb.2007.01.031

2hbh, resolution 2.65Å

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