1K4W

X-ray structure of the orphan nuclear receptor ROR beta ligand-binding domain in the active conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray structure of the orphan nuclear receptor RORbeta ligand-binding domain in the active conformation.

Stehlin, C.Wurtz, J.M.Steinmetz, A.Greiner, E.Schule, R.Moras, D.Renaud, J.P.

(2001) EMBO J. 20: 5822-5831

  • DOI: 10.1093/emboj/20.21.5822

  • PubMed Abstract: 
  • The retinoic acid-related orphan receptor beta (RORbeta) exhibits a highly restricted neuronal-specific expression pattern in brain, retina and pineal gland. So far, neither a natural RORbeta target gene nor a functional ligand have been identified, ...

    The retinoic acid-related orphan receptor beta (RORbeta) exhibits a highly restricted neuronal-specific expression pattern in brain, retina and pineal gland. So far, neither a natural RORbeta target gene nor a functional ligand have been identified, and the physiological role of the receptor is not well understood. We present the crystal structure of the ligand-binding domain (LBD) of RORbeta containing a bound stearate ligand and complexed with a coactivator peptide. In the crystal, the monomeric LBD adopts the canonical agonist-bound form. The fatty acid ligand-coactivator peptide combined action stabilizes the transcriptionally active conformation. The large ligand-binding pocket is strictly hydrophobic on the AF-2 side and more polar on the beta-sheet side where the carboxylate group of the ligand binds. Site-directed mutagenesis experiments validate the significance of the present structure. Homology modeling of the other isotypes will help to design isotype-selective agonists and antagonists that can be used to characterize the physiological functions of RORs. In addition, our crystallization strategy can be extended to other orphan nuclear receptors, providing a powerful tool to delineate their functions.


    Related Citations: 
    • Orphan Nuclear Receptors: from Gene to Function
      Giguere, V.
      (1999) Endocr.Rev. 20: 689
    • Nuclear orphan receptors: the search for novel ligands and signaling pathways
      Willy, P.J.,Mangelsdorf, D.J.
      (1998) Hormones and Signaling 1: 307
    • Structural Studies on Nuclear Receptors
      Renaud, J.P.,Moras, D.
      (2000) Cell.Mol.Life Sci. 57: 1748


    Organizational Affiliation

    Laboratoire de Biologie et Génomique Structurales (CNRS Unité Propre de Recherche 9004), Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS/INSERM/Université Louis Pasteur), 1 rue Laurent Fries, BP 163, 67404 Illkirch, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor ROR-beta
A
252Rattus norvegicusGene Names: Rorb (Nr1f2, Rzrb)
Find proteins for P45446 (Rattus norvegicus)
Go to UniProtKB:  P45446
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
steroid receptor coactivator-1
B
15Homo sapiensGene Names: NCOA1 (BHLHE74, SRC1)
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to Gene View: NCOA1
Go to UniProtKB:  Q15788
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STE
Query on STE

Download SDF File 
Download CCD File 
A
STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.302α = 90.00
b = 58.489β = 90.00
c = 106.036γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-04-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance