1N4H

Characterization of ligands for the orphan nuclear receptor RORbeta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

All-trans retinoic acid is a ligand for the orphan nuclear receptor RORbeta

Stehlin-Gaon, C.Willmann, D.Zeyer, D.Sanglier, S.Van Dorsselaer, A.Renaud, J.-P.Moras, D.Schuele, R.

(2003) Nat Struct Biol 10: 820-825

  • DOI: 10.1038/nsb979
  • Primary Citation of Related Structures:  
    1N4H, 1NQ7

  • PubMed Abstract: 
  • Retinoids regulate gene expression through binding to the nuclear retinoic acid receptors (RARs) and retinoid X receptors (RXRs). In contrast, no ligands for the retinoic acid receptor-related orphan receptors beta and gamma (ROR beta and gamma) have been identified, yet structural data and structure-function analyses indicate that ROR beta is a ligand-regulated nuclear receptor ...

    Retinoids regulate gene expression through binding to the nuclear retinoic acid receptors (RARs) and retinoid X receptors (RXRs). In contrast, no ligands for the retinoic acid receptor-related orphan receptors beta and gamma (ROR beta and gamma) have been identified, yet structural data and structure-function analyses indicate that ROR beta is a ligand-regulated nuclear receptor. Using nondenaturing mass spectrometry and scintillation proximity assays we found that all-trans retinoic acid (ATRA) and several retinoids bind to the ROR beta ligand-binding domain (LBD). The crystal structures of the complex with ATRA and with the synthetic analog ALRT 1550 reveal the binding modes of these ligands. ATRA and related retinoids inhibit ROR beta but not ROR alpha transcriptional activity suggesting that high-affinity, subtype-specific ligands could be designed for the identification of ROR beta target genes. Our results identify ROR beta as a retinoid-regulated nuclear receptor, providing a novel pathway for retinoid action.


    Related Citations: 
    • 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
    • Crystal structure of the RAR-gamma ligand-binding domain bound to all-trans retinoic acid
      Renaud, J.P., Rochel, N., Ruff, M., Vivat, V., Chambon, P., Gronemeyer, H., Moras, D.
      (1995) Nature 378: 681

    Organizational Affiliation

    Département de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 rue Laurent Fries, 67404 Illkirch, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear Receptor ROR-beta A259Rattus norvegicusMutation(s): 0 
Gene Names: RZR-betaRorbNr1f2Rzrb
Find proteins for P45446 (Rattus norvegicus)
Explore P45446 
Go to UniProtKB:  P45446
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Steroid Receptor Coactivator-1 B15N/AMutation(s): 0 
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS:  Q15788
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
REA
Query on REA

Download Ideal Coordinates CCD File 
A
RETINOIC ACID
C20 H28 O2
SHGAZHPCJJPHSC-YCNIQYBTSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
REAKi :  280   nM  PDBBind
REAKd:  280   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.199α = 90
b = 58.125β = 90
c = 106.039γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-23
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance