PDBsum entry 1n4h

Hormone/growth factor

PDB id: 1n4h

Contents

Protein chain

244 a.a. *

Ligands

HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-GLU

REA

Waters ×113

* Residue conservation analysis

PDB id:

1n4h

Name:

Hormone/growth factor

Title:

Characterization of ligands for the orphan nuclear receptor rorbeta

Structure:

Nuclear receptor ror-beta. Chain: a. Fragment: ligand-binding domain. Synonym: nuclear receptor rzr-beta. Engineered: yes. Steroid receptor coactivator-1. Chain: b. Fragment: nr-2 box. Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: rzr-beta. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_tissue: brain. Synthetic: yes. Other_details: the peptide was chemically synthesized. The sequence

Biol. unit:

Dimer (from PQS)

Resolution:

2.10Å R-factor: 0.217 R-free: 0.255

Authors:

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

Key ref:

C.Stehlin-Gaon et al. (2003). All-trans retinoic acid is a ligand for the orphan nuclear receptor ROR beta. Nat Struct Biol, 10, 820-825. PubMed id: 12958591 DOI: 10.1038/nsb979

Date:

31-Oct-02 Release date: 23-Sep-03

Protein chain

P45446  (RORB_RAT) -  Nuclear receptor ROR-beta from Rattus norvegicus

Seq: 470 a.a.

Struc: 244 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1038/nsb979

Nat Struct Biol 10:820-825 (2003)

PubMed id: 12958591

All-trans retinoic acid is a ligand for the orphan nuclear receptor ROR beta.

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

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.

Selected figure(s)

Figure 1.
Figure 1. Nondenaturing ESI-MS analysis of ligand binding to ROR . (a) ROR -stearate complex (ROR -STE): before addition of any ligand, 90% of the detected species correspond to the ROR -STE complex and 10% are related to unliganded ROR . (b) ROR -ATRA complex: after addition of 2.5 molar equivalents of ATRA (molecular mass = 300.4 Da), the only detected species corresponds to the ROR -ATRA complex. Neither unliganded ROR nor the ROR -STE complex is present in the ESI mass spectrum. (c) ROR -ALRT 1550 complex (ROR -ALRT): after addition of 2.5 molar equivalents of ALRT (molecular mass = 340.5 Da), the only detected species corresponds to the ROR -ALRT complex. Neither unliganded ROR nor the ROR -STE complex is present in the ESI mass spectrum. The ESI-MS measured masses for the different complexes are: 31,034.5 0.5 Da for ROR , 31,321.4 0.9 Da for ROR -STE, 31,334.6 1.3 Da for ROR -ATRA and 31,373.9 0.8 Da for ROR -ALRT. Asterisk represents ROR without the His[6]-tag; G, gluconoylation of the His[6]-tag; PG, phosphogluconoylation of the His[6]-tag28.

Figure 2.
Figure 2. Crystal structures of the ROR LBD in complex with ATRA and ALRT. (a) Stereo view of the backbone superposition of the structures of the ROR LBD (yellow) in complex with stearate (orange) and the SRC-1 peptide (red) (PDB entry 1K4W) and of the ROR LBD (green) in complex with ATRA (dark blue) and the SRC-1 peptide. (b) Electron density omit maps of the bound ligands. The maps were calculated at 2.1 Å for ATRA (left) and 1.5 Å for ALRT (right). Contour levels are 2.0 and 2.5 , respectively; labels refer to the canonical helix numbering. (c) Anchoring of the carboxylate of ATRA in two different LBDs. Left, ATRA (yellow) and stearate (orange) in ROR ; the superposition was made on the protein atoms. Right, ATRA in hRAR (PDB entry 2LBD). In ROR , ATRA forms two water mediated hydrogen bonds to Arg306 and Arg309 whereas in RAR it forms one direct hydrogen bond to Arg278. (d) Stereo view of the superposition of stearate (orange), ATRA (yellow) and ALRT (green) in the ROR ligand-binding pocket. The protein atoms follow the standard color code.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 820-825) copyright 2003.

Figures were selected by an automated process.