3W5P

Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of complexes of vitamin D receptor ligand-binding domain with lithocholic acid derivatives.

Masuno, H.Ikura, T.Morizono, D.Orita, I.Yamada, S.Shimizu, M.Ito, N.

(2013) J.Lipid Res. 54: 2206-2213

  • DOI: 10.1194/jlr.M038307
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The secondary bile acid lithocholic acid (LCA) and its derivatives act as selective modulators of the vitamin D receptor (VDR), although their structures fundamentally differ from that of the natural hormone 1α,25-dihydroxyvitamin D3 [1,25(OH)2D3)]. ...

    The secondary bile acid lithocholic acid (LCA) and its derivatives act as selective modulators of the vitamin D receptor (VDR), although their structures fundamentally differ from that of the natural hormone 1α,25-dihydroxyvitamin D3 [1,25(OH)2D3)]. Here, we have determined the crystal structures of the ligand-binding domain of rat VDR (VDR-LBD) in ternary complexes with a synthetic partial peptide of the coactivator MED1 (mediator of RNA polymerase II transcription subunit 1) and four ligands, LCA, 3-keto LCA, LCA acetate, and LCA propionate, with the goal of elucidating their agonistic mechanism. LCA and its derivatives bind to the same ligand-binding pocket (LBP) of VDR-LBD that 1,25(OH)2D3 binds to, but in the opposite orientation; their A-ring is positioned at the top of the LBP, whereas their acyclic tail is located at the bottom of the LBP. However, most of the hydrophobic and hydrophilic interactions observed in the complex with 1,25(OH)2D3 are reproduced in the complexes with LCA and its derivatives. Additional interactions between VDR-LBD and the C-3 substituents of the A-ring are also observed in the complexes with LCA and its derivatives. These may result in the observed difference in the potency among the LCA-type ligands.


    Organizational Affiliation

    Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 receptor
A
271Rattus norvegicusMutation(s): 0 
Gene Names: Vdr (Nr1i1)
Find proteins for P13053 (Rattus norvegicus)
Go to UniProtKB:  P13053
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 1
C
13Homo sapiensMutation(s): 0 
Gene Names: MED1 (ARC205, CRSP1, CRSP200, DRIP205, DRIP230, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2)
Find proteins for Q15648 (Homo sapiens)
Go to Gene View: MED1
Go to UniProtKB:  Q15648
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4OA
Query on 4OA

Download SDF File 
Download CCD File 
A
(3beta,5beta,14beta,17alpha)-3-hydroxycholan-24-oic acid
Lithocholic acid
C24 H40 O3
SMEROWZSTRWXGI-HVATVPOCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.233 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 154.509α = 90.00
b = 42.371β = 96.79
c = 41.649γ = 90.00
Software Package:
Software NamePurpose
SERGUIdata collection
CNSrefinement
CNSphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2014-01-29
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description