1NQ7

Characterization of ligands for the orphan nuclear receptor RORbeta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.201 

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.Mol.Biol. 10: 820-825

  • DOI: 10.1038/nsb979
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEAR RECEPTOR ROR-BETA
A
244Rattus norvegicusMutation(s): 0 
Gene Names: Rorb (Nr1f2, Rzrb)
Find proteins for P45446 (Rattus norvegicus)
Go to UniProtKB:  P45446
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
STEROID RECEPTOR COACTIVATOR-1
B
10Homo sapiensMutation(s): 0 
Gene 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
ARL
Query on ARL

Download SDF File 
Download CCD File 
A
7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID
C23 H32 O2
JMPZTWDLOGTBPM-OUQSKUGOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ARLKi: 160 nM BINDINGMOAD
ARLKi: 160 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.823α = 90.00
b = 58.343β = 90.00
c = 105.668γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance