1NQ7

Characterization of ligands for the orphan nuclear receptor RORbeta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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.


    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEAR RECEPTOR ROR-BETAA244Rattus norvegicusMutation(s): 0 
Gene Names: Nr1f2RorbRzrb
UniProt
Find proteins for P45446 (Rattus norvegicus)
Explore P45446 
Go to UniProtKB:  P45446
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45446
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
STEROID RECEPTOR COACTIVATOR-1B10N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15788
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARL
Query on ARL

Download Ideal Coordinates CCD File 
C [auth A]7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID
C23 H32 O2
JMPZTWDLOGTBPM-OUQSKUGOSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ARL PDBBind:  1NQ7 Ki: 160 (nM) from 1 assay(s)
Binding MOAD:  1NQ7 Ki: 160 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.823α = 90
b = 58.343β = 90
c = 105.668γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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