3NSQ

Crystal structure of tetrameric RXRalpha-LBD complexed with antagonist danthron


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.265 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Danthron functions as a retinoic X receptor antagonist by stabilizing tetramers of the receptor.

Zhang, H.Zhou, R.Li, L.Chen, J.Chen, L.Li, C.Ding, H.Yu, L.Hu, L.Jiang, H.Shen, X.

(2011) J Biol Chem 286: 1868-1875

  • DOI: 10.1074/jbc.M110.166215
  • Primary Citation of Related Structures:  
    3NSP, 3NSQ

  • PubMed Abstract: 
  • Retinoic X receptor (RXR) is a promising target for drug discovery against cancer and metabolic syndromes. Here, we identified a specific RXRα antagonist, danthron, from the traditional Chinese medicine rhubarb. Danthron repressed all tested RXRα-involved response element transcription, including the RXRE, PPRE, FXRE, and LXRE ...

    Retinoic X receptor (RXR) is a promising target for drug discovery against cancer and metabolic syndromes. Here, we identified a specific RXRα antagonist, danthron, from the traditional Chinese medicine rhubarb. Danthron repressed all tested RXRα-involved response element transcription, including the RXRE, PPRE, FXRE, and LXRE. Results from native PAGE and isothermal titration calorimetry (ITC)-based assays indicated that danthron bound to the tetrameric RXRα-LBD in a specific stoichimetric ratio, and such a binding could influence the corepressor SMRT affinity to the receptor. Additionally, a unique tetrameric structure of the apo-RXRα ligand-binding domain (LBD) was determined, which exhibited a larger tetramer interface and different ligand-binding pocket size compared with the one previously reported. Together with the biochemical and biophysical results, the determined crystal structure of danthron-soaked RXRα-LBD suggested a new mechanism for danthron antagonism to tetrameric RXRα. Moreover, the in vivo efficient improvement of insulin sensitivity by danthron was observed in diet-induced obese (DIO) mice. Thus, our findings were expected to supply new insights into the structural basis of RXRα antagonist for its further potential therapeutic application.


    Organizational Affiliation

    State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoid X receptor, alphaA, B240Homo sapiensMutation(s): 0 
Gene Names: RXRANR2B1RP11-473E2.1-002hCG_18150
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
NIH Common Fund Data Resources
PHAROS:  P19793
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CHZ
Query on CHZ

Download Ideal Coordinates CCD File 
C [auth B]1,8-dihydroxyanthracene-9,10-dione
C14 H8 O4
QBPFLULOKWLNNW-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CHZKd :  6200   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.265 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.026α = 90
b = 99.924β = 90
c = 47.201γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-11
    Changes: Database references