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PDBsum entry 1n4h
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Hormone/growth factor
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PDB id
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1n4h
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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All-Trans retinoic acid is a ligand for the orphan nuclear receptor ror beta.
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Authors
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C.Stehlin-Gaon,
D.Willmann,
D.Zeyer,
S.Sanglier,
A.Van dorsselaer,
J.P.Renaud,
D.Moras,
R.Schüle.
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Ref.
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Nat Struct Biol, 2003,
10,
820-825.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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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.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2003,
10,
820-825)
copyright 2003.
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Secondary reference #1
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Title
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X-Ray structure of the orphan nuclear receptor rorbeta ligand-Binding domain in the active conformation.
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Authors
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C.Stehlin,
J.M.Wurtz,
A.Steinmetz,
E.Greiner,
R.Schüle,
D.Moras,
J.P.Renaud.
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Ref.
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EMBO J, 2001,
20,
5822-5831.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2 Schematic representation of the rROR LBD
in complex with stearate (ball-and-stick) and a SRC-1 peptide
(ribbon representation). The kink in H10 has been emphasized by
breaking H10 into two segments.
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Figure 5.
Figure 5 Homology modeling of ROR  ,
ROR and
DHR3 LBDs, showing the non-conserved residues affecting the
pocket's shape. Figures 2, 3A, 4 and 5 were prepared with SETOR
(Evans, 1993).
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by Macmillan Publishers Ltd
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Secondary reference #2
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Title
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Crystal structure of the rar-Gamma ligand-Binding domain bound to all-Trans retinoic acid.
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Authors
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J.P.Renaud,
N.Rochel,
M.Ruff,
V.Vivat,
P.Chambon,
H.Gronemeyer,
D.Moras.
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Ref.
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Nature, 1995,
378,
681-689.
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PubMed id
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