3VT6

Crystal structure of rat VDR-LBD with 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands.

Nakabayashi, M.Tsukahara, Y.Iwasaki-Miyamoto, Y.Mihori-Shimazaki, M.Yamada, S.Inaba, S.Oda, M.Shimizu, M.Makishima, M.Tokiwa, H.Ikura, T.Ito, N.

(2013) J.Med.Chem. 56: 6745-6760

  • DOI: 10.1021/jm400537h
  • Primary Citation of Related Structures:  3VT3, 3VT4, 3VT5, 3VT7, 3VT8, 3VT9

  • PubMed Abstract: 
  • The vitamin D receptor (VDR), a member of the nuclear receptor superfamily, functions as a ligand-dependent transcription factor for various genes. Hereditary vitamin D-resistant rickets (HVDRR), an autosomal recessive disease, is caused by mutations ...

    The vitamin D receptor (VDR), a member of the nuclear receptor superfamily, functions as a ligand-dependent transcription factor for various genes. Hereditary vitamin D-resistant rickets (HVDRR), an autosomal recessive disease, is caused by mutations in the VDR. In particular, the missense mutations R274L and W286R in the ligand-binding domain of the VDR can severely reduce or even eliminate natural hormone responsiveness. Here, we report a crystal structure analysis of the R270L and W282R mutants of rat VDR (human R274L and W286R, respectively) in complex with the natural hormone and synthetic ligands. We also studied the folding properties of the mutant proteins by using circular dichroism spectra. Our study indicates that these mutations result in only local structural modifications. We discuss why these mutations disrupt the VDR function and provide clues to develop effective ligands for the treatment of HVDRR.


    Organizational Affiliation

    Graduate School of Biomedical Science, ‡Institute of Biomaterials and Bioengineering, and §Medical Research Institute, Tokyo Medical and Dental University , Bunkyo-ku, Tokyo 113-8510, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 receptor
A
271Rattus norvegicusGene Names: Vdr (Nr1i1)
Find proteins for P13053 (Rattus norvegicus)
Go to UniProtKB:  P13053
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
COACTIVATOR PEPTIDE DRIP
C
13N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5YI
Query on 5YI

Download SDF File 
Download CCD File 
A
(1R,2Z,3R,5E,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol
C28 H44 O4 S
PIRFBNFXEQEXIT-XXUXJEHWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 153.734α = 90.00
b = 42.724β = 95.55
c = 42.271γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
HKL-2000data scaling
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-09-11
    Type: Database references
  • Version 1.2: 2014-02-12
    Type: Database references