2P1V

Crystal structure of the ligand binding domain of the retinoid X receptor alpha in complex with 3-(2'-propoxy)-tetrahydronaphtyl cinnamic acid and a fragment of the coactivator TIF-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Modulators of the structural dynamics of the retinoid X receptor to reveal receptor function.

Nahoum, V.Perez, E.Germain, P.Rodriguez-Barrios, F.Manzo, F.Kammerer, S.Lemaire, G.Hirsch, O.Royer, C.A.Gronemeyer, H.de Lera, A.R.Bourguet, W.

(2007) Proc.Natl.Acad.Sci.Usa 104: 17323-17328

  • DOI: 10.1073/pnas.0705356104
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Retinoid X receptors (RXRalpha, -beta, and -gamma) occupy a central position in the nuclear receptor superfamily, because they form heterodimers with many other family members and hence are involved in the control of a variety of (patho)physiologic p ...

    Retinoid X receptors (RXRalpha, -beta, and -gamma) occupy a central position in the nuclear receptor superfamily, because they form heterodimers with many other family members and hence are involved in the control of a variety of (patho)physiologic processes. Selective RXR ligands, referred to as rexinoids, are already used or are being developed for cancer therapy and have promise for the treatment of metabolic diseases. However, important side effects remain associated with existing rexinoids. Here we describe the rational design and functional characterization of a spectrum of RXR modulators ranging from partial to pure antagonists and demonstrate their utility as tools to probe the implication of RXRs in cell biological phenomena. One of these ligands renders RXR activity particularly sensitive to coactivator levels and has the potential to act as a cell-specific RXR modulator. A combination of crystallographic and fluorescence anisotropy studies reveals the molecular details accounting for the agonist-to-antagonist transition and provides direct experimental evidence for a correlation between the pharmacological activity of a ligand and its impact on the structural dynamics of the activation helix H12. Using RXR and its cognate ligands as a model system, our correlative analysis of 3D structures and dynamic data provides an original view on ligand actions and enables the establishment of mechanistic concepts, which will aid in the development of selective nuclear receptor modulators.


    Organizational Affiliation

    Institut National de la Santé et de la Recherche Médicale, U554, 34090 Montpellier, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor RXR-alpha
A
240Homo 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
Nuclear receptor coactivator 2 peptide
B
13Homo sapiensMutation(s): 0 
Gene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5TN
Query on 5TN

Download SDF File 
Download CCD File 
A
(2E)-3-[4-HYDROXY-3-(5,5,8,8-TETRAMETHYL-3-PROPOXY-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)PHENYL]ACRYLIC ACID
C26 H32 O4
DJVKZKGDIQNPRJ-CSKARUKUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 64.148α = 90.00
b = 64.148β = 90.00
c = 113.153γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
DNAdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance