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- PDB-1nq7: Characterization of ligands for the orphan nuclear receptor RORbeta -

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Basic information

Entry
Database: PDB / ID: 1nq7
TitleCharacterization of ligands for the orphan nuclear receptor RORbeta
Components
  • NUCLEAR RECEPTOR ROR-BETA
  • STEROID RECEPTOR COACTIVATOR-1
KeywordsTRANSCRIPTION / LIGAND-BINDING DOMAIN / RETINOIDS / RETINOIC ACID / SYNTHETIC LIGAND / ANTAGONIST
Function / homology
Function and homology information


retinal rod cell development / melatonin receptor activity / amacrine cell differentiation / retinal rod cell differentiation / retinal cone cell development / Nuclear Receptor transcription pathway / eye photoreceptor cell development / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway ...retinal rod cell development / melatonin receptor activity / amacrine cell differentiation / retinal rod cell differentiation / retinal cone cell development / Nuclear Receptor transcription pathway / eye photoreceptor cell development / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / male mating behavior / hypothalamus development / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / progesterone receptor signaling pathway / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / negative regulation of osteoblast differentiation / estrous cycle / nuclear retinoid X receptor binding / histone acetyltransferase activity / cellular response to hormone stimulus / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone acetyltransferase / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to hormone / estrogen receptor signaling pathway / cellular response to retinoic acid / lactation / : / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / visual perception / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / cerebellum development / nuclear estrogen receptor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / circadian rhythm / Cytoprotection by HMOX1 / regulation of circadian rhythm / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / sequence-specific double-stranded DNA binding / : / response to estradiol / HATs acetylate histones / retina development in camera-type eye / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription coactivator activity / protein dimerization activity / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain ...Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-ARL / : / Nuclear receptor ROR-beta / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsStehlin-Gaon, C. / Willmann, D. / Sanglier, S. / Van Dorsselaer, A. / Renaud, J.-P. / Moras, D. / Schuele, R.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: All-trans retinoic acid is a ligand for the orphan nuclear receptor RORbeta
Authors: Stehlin-Gaon, C. / Willmann, D. / Zeyer, D. / Sanglier, S. / Van Dorsselaer, A. / Renaud, J.-P. / Moras, D. / Schuele, R.
History
DepositionJan 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEAR RECEPTOR ROR-BETA
B: STEROID RECEPTOR COACTIVATOR-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7993
Polymers29,4582
Non-polymers3401
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-7 kcal/mol
Surface area12360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.823, 58.343, 105.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NUCLEAR RECEPTOR ROR-BETA / NUCLEAR RECEPTOR RZR-BETA


Mass: 28167.613 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: NR1F2 / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P45446
#2: Protein/peptide STEROID RECEPTOR COACTIVATOR-1


Mass: 1290.556 Da / Num. of mol.: 1 / Fragment: SECOND NR-BOX / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
References: GenBank: 1906028, UniProt: Q15788*PLUS
#3: Chemical ChemComp-ARL / 7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID


Mass: 340.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H32O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG6000, NACL, TRIS-HCL, CHAPS, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown / Details: Potier, N., (2003) Protein Sci., 12, 725.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.01 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 53047 / Num. obs: 52613 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.061 / Net I/σ(I): 32
Reflection shellResolution: 1.5→1.55 Å / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / Num. obs: 53123 / % possible obs: 100 % / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 13

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K4W

1k4w


Resolution: 1.5→19.87 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2668 5.1 %RANDOM
Rwork0.201 ---
obs0.201 52613 99 %-
all-53047 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.2813 Å2 / ksol: 0.304355 e/Å3
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20 Å2
2--1.27 Å20 Å2
3----2.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.5→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 25 381 2472
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.631.5
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scbond_it4.162
X-RAY DIFFRACTIONc_scangle_it5.852.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 456 5.4 %
Rwork0.222 8038 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3alrt.paramalrt.top
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.077
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

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