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- PDB-1n83: Crystal Structure of the complex between the Orphan Nuclear Hormo... -

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Basic information

Entry
Database: PDB / ID: 1n83
TitleCrystal Structure of the complex between the Orphan Nuclear Hormone Receptor ROR(alpha)-LBD and Cholesterol
ComponentsNuclear receptor ROR-alpha
KeywordsLIPID BINDING PROTEIN / three-layered alpha helical sandwich / receptor / transcription regulation / nuclear protein / DNA binding
Function / homology
Function and homology information


cGMP metabolic process / cerebellar Purkinje cell differentiation / muscle cell differentiation / cerebellar granule cell precursor proliferation / T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / triglyceride homeostasis / intracellular receptor signaling pathway ...cGMP metabolic process / cerebellar Purkinje cell differentiation / muscle cell differentiation / cerebellar granule cell precursor proliferation / T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / triglyceride homeostasis / intracellular receptor signaling pathway / positive regulation of circadian rhythm / oxysterol binding / regulation of smoothened signaling pathway / regulation of macrophage activation / negative regulation of fat cell differentiation / regulation of glucose metabolic process / positive regulation of vascular endothelial growth factor production / cellular response to interleukin-1 / negative regulation of canonical NF-kappaB signal transduction / RORA activates gene expression / nitric oxide biosynthetic process / xenobiotic metabolic process / cholesterol homeostasis / transcription corepressor binding / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / SUMOylation of intracellular receptors / Heme signaling / transcription coactivator binding / PPARA activates gene expression / negative regulation of inflammatory response / beta-catenin binding / Nuclear Receptor transcription pathway / nuclear receptor activity / Circadian Clock / cellular response to tumor necrosis factor / cellular response to hypoxia / angiogenesis / Interleukin-4 and Interleukin-13 signaling / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / 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
CHOLESTEROL / Nuclear receptor ROR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.63 Å
AuthorsKallen, J.A. / Schlaeppi, J.M. / Bitsch, F. / Geisse, S. / Geiser, M. / Delhon, I. / Fournier, B.
CitationJournal: Structure / Year: 2002
Title: X-ray Structure of hROR(alpha) LBD at 1.63A: Structural and Functional data that Cholesterol or a Cholesterol derivative is the natural ligand of ROR(alpha)
Authors: Kallen, J.A. / Schlaeppi, J.M. / Bitsch, F. / Geisse, S. / Geiser, M. / Delhon, I. / Fournier, B.
History
DepositionNov 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor ROR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9012
Polymers31,5141
Non-polymers3871
Water7,548419
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.800, 49.700, 60.500
Angle α, β, γ (deg.)90.00, 98.40, 90.00
Int Tables number4
Space group name H-MP1211

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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, residues 304-556
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P35398
#2: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.32 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, sodium acetate, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris-HCl1reservoirpH8.4
219 %PEG60001reservoir
30.2 M1reservoirCaCl2

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8727 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 30, 2001
RadiationMonochromator: Si Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8727 Å / Relative weight: 1
ReflectionResolution: 1.63→15 Å / Num. all: 38783 / Num. obs: 38783 / % possible obs: 95.36 % / Observed criterion σ(I): 0 / Redundancy: 3.65 % / Biso Wilson estimate: 22.1 Å2 / Rsym value: 0.04 / Net I/σ(I): 32
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 2775 / Rsym value: 0.433 / % possible all: 67.3
Reflection
*PLUS
Num. measured all: 141730 / Rmerge(I) obs: 0.04

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMAC5refinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.63→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.74 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.098 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22277 1913 5 %RANDOM
Rwork0.20067 ---
all0.2018 38477 --
obs0.2018 36564 95.36 %-
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: 22.739 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å2-0.61 Å2
2---0.12 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 1.63→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 28 419 2513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212141
X-RAY DIFFRACTIONr_bond_other_d0.0010.021917
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.9642890
X-RAY DIFFRACTIONr_angle_other_deg0.65134474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2983250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13215411
X-RAY DIFFRACTIONr_chiral_restr0.0680.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022308
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02431
X-RAY DIFFRACTIONr_nbd_refined0.2410.3582
X-RAY DIFFRACTIONr_nbd_other0.1930.31962
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.5244
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.060.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.349
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.516
X-RAY DIFFRACTIONr_mcbond_it0.6941.51252
X-RAY DIFFRACTIONr_mcangle_it1.3522023
X-RAY DIFFRACTIONr_scbond_it2.0863889
X-RAY DIFFRACTIONr_scangle_it3.4294.5867
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 112
Rwork0.26 2276
Refinement
*PLUS
Lowest resolution: 15 Å / Num. reflection obs: 36570 / Num. reflection Rfree: 1907 / % reflection Rfree: 5 % / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.11

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