5MJ5

Crystal structure of the Retinoid X Receptor alpha in complex with synthetichonokiol derivative 3 and a fragment of the TIF2 co-activator.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Ligand Dependent Switch from RXR Homo- to RXR-NURR1 Heterodimerization.

Scheepstra, M.Andrei, S.A.de Vries, R.M.J.M.Meijer, F.A.Ma, J.N.Burstein, E.S.Olsson, R.Ottmann, C.Milroy, L.G.Brunsveld, L.

(2017) ACS Chem Neurosci 8: 2065-2077

  • DOI: 10.1021/acschemneuro.7b00216
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Retinoid X receptors (RXRs) play key roles in many physiological processes in both the periphery and central nervous system. In addition, RXRs form heterodimers with other nuclear receptors to exert their physiological effects. The nuclear receptor r ...

    Retinoid X receptors (RXRs) play key roles in many physiological processes in both the periphery and central nervous system. In addition, RXRs form heterodimers with other nuclear receptors to exert their physiological effects. The nuclear receptor related 1 protein (NURR1) is particularly interesting because of its role in promoting differentiation and survival of dopamine neurons. However, only a small number of RXR-heterodimer selective modulators are available, with limited chemical diversity. This work describes the synthesis, biochemical evaluation, and structural elucidation of a novel series of RXR ligands with strongly biased interactions with RXRα-NURR1 heterodimers. Targeted modifications to the small molecule biaryl scaffold caused local RXRα side-chain disturbances and displacement of secondary structural elements upon ligand binding. This resulted in the repositioning of protein helices in the heterodimer interface of RXRα, alterations in homo- versus heterodimer formation, and modulation of activation function 2 (AF2). The data provide a rationale for the design of RXR ligands consisting of a highly conserved hydrophilic region, strongly contributing to the ligand affinity, and a variable hydrophobic region, which efficiently probes the effects of structural changes at the level of the ligand on co-regulator recruitment or the RXRα-NURR1 dimerization interface.


    Organizational Affiliation

    Department of Biomedical Engineering and Institute for Complex Molecular Systems, Laboratory of Chemical Biology, Technische Universiteit Eindhoven , Den Dolech 2, 5612 AZ Eindhoven, The Netherlands.,Chemical Biology & Therapeutics, Department of Experimental Medical Science, Lund University , SE-221 00 Lund, Sweden.,ACADIA Pharmaceuticals Inc., San Diego, California 92130, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor RXR-alpha
A
229Homo sapiensMutation(s): 0 
Gene Names: RXRA (NR2B1)
Find proteins for P19793 (Homo sapiens)
Go to Gene View: RXRA
Go to UniProtKB:  P19793
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LYS-HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-ASP-SER
B
13N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7O0
Query on 7O0

Download SDF File 
Download CCD File 
A
(~{E})-3-[4-oxidanyl-3-[3-(phenylmethyl)phenyl]phenyl]prop-2-enoic acid
C22 H18 O3
WOWLBKWVURQFNH-ZRDIBKRKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.197 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.159α = 90.00
b = 68.159β = 90.00
c = 109.719γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NWONetherlandsECHO 711011017

Revision History 

  • Version 1.0: 2017-11-08
    Type: Initial release