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- PDB-1s0x: Crystal structure of the human RORalpha ligand binding domain in ... -

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Basic information

Entry
Database: PDB / ID: 1s0x
TitleCrystal structure of the human RORalpha ligand binding domain in complex with cholesterol sulfate at 2.2A
ComponentsNuclear receptor ROR-alpha
Keywordshormone/growth factor receptor / THREE-LAYERED ALPHA HELICAL SANDWICH / NUCLEAR HORMONE RECEPTOR / ORPHAN RECEPTOR / LIGAND BINDING DOMAIN / hormone-growth factor receptor COMPLEX
Function / homology
Function and homology information


cGMP metabolic process / cerebellar Purkinje cell differentiation / cerebellar granule cell precursor proliferation / intracellular receptor signaling pathway / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-activated transcription factor activity / positive regulation of circadian rhythm / oxysterol binding ...cGMP metabolic process / cerebellar Purkinje cell differentiation / cerebellar granule cell precursor proliferation / intracellular receptor signaling pathway / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-activated transcription factor activity / positive regulation of circadian rhythm / oxysterol binding / muscle cell differentiation / regulation of smoothened signaling pathway / triglyceride homeostasis / regulation of macrophage activation / negative regulation of fat cell differentiation / cellular response to interleukin-1 / regulation of glucose metabolic process / positive regulation of vascular endothelial growth factor production / negative regulation of canonical NF-kappaB signal transduction / nitric oxide biosynthetic process / RORA activates gene expression / xenobiotic metabolic process / transcription corepressor binding / cholesterol homeostasis / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / SUMOylation of intracellular receptors / Heme signaling / PPARA activates gene expression / transcription coactivator binding / negative regulation of inflammatory response / Nuclear Receptor transcription pathway / beta-catenin binding / nuclear receptor activity / Circadian Clock / cellular response to tumor necrosis factor / cellular response to hypoxia / Interleukin-4 and Interleukin-13 signaling / angiogenesis / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / 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
CHOLEST-5-EN-3-YL HYDROGEN SULFATE / Nuclear receptor ROR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsKallen, J. / Schlaeppi, J.M. / Bitsch, F. / Delhon, I. / Fournier, B.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of the human RORalpha Ligand binding domain in complex with cholesterol sulfate at 2.2 A
Authors: Kallen, J. / Schlaeppi, J.M. / Bitsch, F. / Delhon, I. / Fournier, B.
#1: Journal: Structure / Year: 2002
Title: X-ray structure of the hRORalpha LBD at 1.63A: Structural and functional data that cholesterol or a cholesterol derivative is the natural ligand of RORalpha
Authors: Kallen, J. / Schlaeppi, J.-M. / Bitsch, F. / Geisse, S. / Geiser, M. / Delhon, I. / Fournier, B.
History
DepositionJan 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor ROR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9812
Polymers31,5141
Non-polymers4671
Water4,612256
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.400, 49.900, 60.700
Angle α, β, γ (deg.)90.00, 97.80, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly is monomer

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Components

#1: Protein Nuclear receptor ROR-alpha / Nuclear receptor RZR-alpha


Mass: 31514.279 Da / Num. of mol.: 1 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RORA, NR1F1, RZRA / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P35398
#2: Chemical ChemComp-C3S / CHOLEST-5-EN-3-YL HYDROGEN SULFATE / CHOLESTEROL-SULFATE


Mass: 466.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.78 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
117.6 mg/mlprotein1drop
20.2 M1reservoirMgCl2
316 MPEG40001reservoir
40.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.92 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 17, 2002
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 16541 / Num. obs: 16541 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 16.2
Reflection shellResolution: 2.2→2.28 Å / % possible all: 99.4
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 57993
Reflection shell
*PLUS
% possible obs: 99.4 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1N83

1n83


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.909 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20874 830 5 %RANDOM
Rwork0.19672 ---
all0.19734 15671 --
obs0.19734 15671 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.919 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å2-0.79 Å2
2---0.15 Å20 Å2
3----2.06 Å2
Refine analyzeLuzzati coordinate error free: 0.181 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 32 256 2354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212145
X-RAY DIFFRACTIONr_bond_other_d0.0010.021917
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9672897
X-RAY DIFFRACTIONr_angle_other_deg0.74334474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3013250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22215411
X-RAY DIFFRACTIONr_chiral_restr0.0790.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022313
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02431
X-RAY DIFFRACTIONr_nbd_refined0.2550.3563
X-RAY DIFFRACTIONr_nbd_other0.2090.31831
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.5186
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3230.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.310.342
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3920.58
X-RAY DIFFRACTIONr_mcbond_it0.8331.51252
X-RAY DIFFRACTIONr_mcangle_it1.66922023
X-RAY DIFFRACTIONr_scbond_it2.5093893
X-RAY DIFFRACTIONr_scangle_it4.2074.5874
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.275 75
Rwork0.295 1130
obs-1130
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.41

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