3A2H image
Entry Detail
PDB ID:
3A2H
Title:
Crystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2009-05-20
Release Date:
2010-05-26
Method Details:
Experimental Method:
Resolution:
2.50 Å
R-Value Free:
0.30
R-Value Work:
0.22
R-Value Observed:
0.23
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Vitamin D3 receptor
Mutations:DEL(165-211) mutant
Chain IDs:A
Chain Length:265
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Description:Mediator of RNA polymerase II transcription subunit 1 peptide
Chain IDs:B
Chain Length:13
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Structural basis of the histidine-mediated vitamin D receptor agonistic and antagonistic mechanisms of (23S)-25-dehydro-1alpha-hydroxyvitamin D(3)-26,23-lactone
Acta Crystallogr.,Sect.D 66 918 926 (2010)
PMID: 20693691 DOI: 10.1107/S0907444910020810

Abstact

TEI-9647 antagonizes vitamin D receptor (VDR) mediated genomic actions of 1alpha,25(OH)2D3 in human cells but is agonistic in rodent cells. The presence of Cys403, Cys410 or of both residues in the C-terminal region of human VDR (hVDR) results in antagonistic action of this compound. In the complexes of TEI-9647 with wild-type hVDR (hVDRwt) and H397F hVDR, TEI-9647 functions as an antagonist and forms a covalent adduct with hVDR according to MALDI-TOF MS. The crystal structures of complexes of TEI-9647 with rat VDR (rVDR), H305F hVDR and H305F/H397F hVDR showed that the agonistic activity of TEI-9647 is caused by a hydrogen-bond interaction with His397 or Phe397 located in helix 11. Both biological activity assays and the crystal structure of H305F hVDR complexed with TEI-9647 showed that the interaction between His305 and TEI-9647 is crucial for antagonist activity. This study indicates the following stepwise mechanism for TEI-9647 antagonism. Firstly, TEI-9647 forms hydrogen bonds to His305, which promote conformational changes in hVDR and draw Cys403 or Cys410 towards the ligand. This is followed by the formation of a 1,4-Michael addition adduct between the thiol (-SH) group of Cys403 or Cys410 and the exo-methylene group of TEI-9647.

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Primary Citation of related structures