1XAP

Structure of the ligand binding domain of the Retinoic Acid Receptor beta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Rational design of RAR-selective ligands revealed by RARbeta crystal structure

Germain, P.Kammerer, S.Perez, E.Peluso-Iltis, C.Tortolani, D.Zusi, F.C.Starrett, J.Lapointe, P.Daris, J.P.Marinier, A.De Lera, A.R.Rochel, N.Gronemeyer, H.

(2004) Embo Rep. 5: 877-882

  • DOI: 10.1038/sj.embor.7400235

  • PubMed Abstract: 
  • The crystal structure of the ligand-binding domain of RARbeta, a suspect tumour suppressor, reveals important features that distinguish it from the two other RAR isotypes. The most striking difference is an extra cavity allowing RARbeta to bind more ...

    The crystal structure of the ligand-binding domain of RARbeta, a suspect tumour suppressor, reveals important features that distinguish it from the two other RAR isotypes. The most striking difference is an extra cavity allowing RARbeta to bind more bulky agonists. Accordingly, we identified a ligand that shows RARbeta selectivity with a 100-fold higher affinity to RARbeta than to alpha or gamma isotypes. The structural differences between the three RAR ligand-binding pockets revealed a rationale explaining how a single retinoid can be at the same time an RARalpha, gamma antagonist and an RARbeta agonist. In addition, we demonstrate how to generate an RARbeta antagonist by gradually modifying the bulkiness of a single substitution. Together, our results provide structural guidelines for the synthesis of RARbeta-selective agonists and antagonists, allowing for the first time to address pharmacologically the tumour suppressor role of RARbeta in vitro and in animal models.


    Organizational Affiliation

    Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/ULP, BP 10142, 67404 Illkirch Cedex, CU de Strasbourg, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor beta
A
267Homo sapiensMutation(s): 0 
Gene Names: RARB (HAP, NR1B2)
Find proteins for P10826 (Homo sapiens)
Go to Gene View: RARB
Go to UniProtKB:  P10826
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TTB
Query on TTB

Download SDF File 
Download CCD File 
A
4-[(1E)-2-(5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)PROP-1-ENYL]BENZOIC ACID
TTNPB
C24 H28 O2
FOIVPCKZDPCJJY-JQIJEIRASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.276α = 90.00
b = 57.808β = 90.00
c = 90.289γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
HKL-2000data collection
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2016-12-28
    Type: Database references