3A9E

Crystal structure of a mixed agonist-bound RAR-alpha and antagonist-bound RXR-alpha heterodimer ligand binding domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Phantom Effect of the Rexinoid LG100754: structural and functional insights

Sato, Y.Ramalanjaona, N.Huet, T.Potier, N.Osz, J.Antony, P.Peluso-Iltis, C.Poussin-Courmontagne, P.Ennifar, E.Mely, Y.Dejaegere, A.Moras, D.Rochel, N.

(2010) PLoS One 5: e15119-e15119

  • DOI: 10.1371/journal.pone.0015119
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Retinoic acid receptors (RARs) and Retinoid X nuclear receptors (RXRs) are ligand-dependent transcriptional modulators that execute their biological action through the generation of functional heterodimers. RXR acts as an obligate dimer partner in ma ...

    Retinoic acid receptors (RARs) and Retinoid X nuclear receptors (RXRs) are ligand-dependent transcriptional modulators that execute their biological action through the generation of functional heterodimers. RXR acts as an obligate dimer partner in many signalling pathways, gene regulation by rexinoids depending on the liganded state of the specific heterodimeric partner. To address the question of the effect of rexinoid antagonists on RAR/RXR function, we solved the crystal structure of the heterodimer formed by the ligand binding domain (LBD) of the RARα bound to its natural agonist ligand (all-trans retinoic acid, atRA) and RXRα bound to a rexinoid antagonist (LG100754). We observed that RARα exhibits the canonical agonist conformation and RXRα an antagonist one with the C-terminal H12 flipping out to the solvent. Examination of the protein-LG100754 interactions reveals that its propoxy group sterically prevents the H12 associating with the LBD, without affecting the dimerization or the active conformation of RAR. Although LG100754 has been reported to act as a 'phantom ligand' activating RAR in a cellular context, our structural data and biochemical assays demonstrate that LG100754 mediates its effect as a full RXR antagonist. Finally we show that the 'phantom ligand effect' of the LG100754 is due to a direct binding of the ligand to RAR that stabilizes coactivator interactions thus accounting for the observed transcriptional activation of RAR/RXR.


    Organizational Affiliation

    Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 1704/Université de Strasbourg, Illkirch, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor RXR-alpha
A
240Mus musculusMutation(s): 0 
Gene Names: RxraNr2b1
Find proteins for P28700 (Mus musculus)
Go to UniProtKB:  P28700

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor alpha
B
269Homo sapiensMutation(s): 0 
Gene Names: RARANR1B1
Find proteins for P10276 (Homo sapiens)
Go to UniProtKB:  P10276
NIH Common Fund Data Resources
PHAROS  P10276
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
13-mer (LXXLL motif) from Nuclear receptor coactivator 2
I
13Homo sapiensMutation(s): 0 
Gene Names: NCOA2BHLHE75SRC2TIF2
Find proteins for Q15596 (Homo sapiens)
Go to UniProtKB:  Q15596
NIH Common Fund Data Resources
PHAROS  Q15596
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
754
Query on 754

Download CCD File 
A
(2E,4E,6Z)-3-methyl-7-(5,5,8,8-tetramethyl-3-propoxy-5,6,7,8-tetrahydronaphthalen-2-yl)octa-2,4,6-trienoic acid
C26 H36 O3
HNODNXQAYXJFMQ-LQUSFLDPSA-N
 Ligand Interaction
REA
Query on REA

Download CCD File 
B
RETINOIC ACID
C20 H28 O2
SHGAZHPCJJPHSC-YCNIQYBTSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
754EC50:  2   nM  BindingDB
754Ki:  1791   nM  BindingDB
754EC50:  4   nM  BindingDB
754EC50:  4   nM  BindingDB
REAIC50:  50000   nM  BindingDB
REAIC50:  50000   nM  BindingDB
754Ki:  8   nM  BindingDB
REAIC50:  50000   nM  BindingDB
754EC50:  10   nM  BindingDB
754EC50:  13   nM  BindingDB
REAIC50:  1000   nM  BindingDB
754Ki:  9   nM  BindingDB
754Ki:  14   nM  BindingDB
REAIC50:  1000   nM  BindingDB
754Ki:  2587   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.3α = 90
b = 105.3β = 90
c = 111.338γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-10-30
    Changes: Database references