Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.67 kDa 
• Atom Count: 2201 
• Modelled Residue Count: 254 
• Deposited Residue Count: 274 
• Unique protein chains: 2

1N4H

Characterization of ligands for the orphan nuclear receptor RORbeta

• PDB DOI: 10.2210/pdb1N4H/pdb

• Classification: HORMONE/GROWTH FACTOR
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-10-31 Released: 2003-09-23 
• Deposition Author(s): Stehlin-Gaon, C., Willmann, D., Sanglier, S., Van Dorsselaer, A., Renaud, J.-P., Moras, D., Schuele, R.

---

Experimental Data Snapshot

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

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

• PubMed: 12958591 
• 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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear Receptor ROR-beta	A	259	Rattus norvegicus	Mutation(s): 0  Gene Names: RZR-beta, Rorb, Nr1f2, Rzrb
UniProt
Find proteins for P45446 (Rattus norvegicus) Explore P45446  Go to UniProtKB:  P45446

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Steroid Receptor Coactivator-1	B	15	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
REA	C [auth A]	RETINOIC ACID C20 H28 O2 SHGAZHPCJJPHSC-YCNIQYBTSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
REA	PDBBind:  1N4H	Ki: 280 (nM) from 1 assay(s)
	Binding MOAD:  1N4H	Kd: 280 (nM) from 1 assay(s)

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 = 52.199	α = 90
b = 58.125	β = 90
c = 106.039	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-10-31 
• Released Date: 2003-09-23 
Deposition Author(s): Stehlin-Gaon, C., Willmann, D., Sanglier, S., Van Dorsselaer, A., Renaud, J.-P., Moras, D., Schuele, R.

Revision History  

• 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