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- PDB-1xnx: Crystal structure of constitutive androstane receptor -

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Basic information

Entry
Database: PDB / ID: 1xnx
TitleCrystal structure of constitutive androstane receptor
Componentsconstitutive androstane receptor
KeywordsLIGAND RECEPTOR/TRANSCRIPTION REGULATION / nuclear receptor / crystal structure / LIGAND RECEPTOR-TRANSCRIPTION REGULATION COMPLEX
Function / homology
Function and homology information


Nuclear Receptor transcription pathway / osteoblast differentiation / nuclear receptor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / cytoskeleton / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II ...Nuclear Receptor transcription pathway / osteoblast differentiation / nuclear receptor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / cytoskeleton / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Thyroid hormone receptor / : / 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 ...Thyroid hormone receptor / : / 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
16,17-ANDROSTENE-3-OL / Nuclear receptor subfamily 1 group I member 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFernandez, E.
CitationJournal: Mol.Cell / Year: 2004
Title: Structure of the murine constitutive androstane receptor complexed to androstenol; a molecular basis for inverse agonism
Authors: Shan, L. / Vincent, J. / Brunzelle, J.S. / Dussault, I. / Lin, M. / Ianculescu, I. / Sherman, M.A. / Forman, B.M. / Fernandez, E.
History
DepositionOct 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Assembly

Deposited unit
A: constitutive androstane receptor
B: constitutive androstane receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8434
Polymers59,2942
Non-polymers5492
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.353, 155.042, 134.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: Protein constitutive androstane receptor / Orphan nuclear receptor NR1I3 / CAR


Mass: 29647.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nr1i3, Car / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: O35627
#2: Chemical ChemComp-ATE / 16,17-ANDROSTENE-3-OL


Mass: 274.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H30O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.91 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 3Xmolar excess of androstenol to purified mCAR LBD and incubate at RT for 1 h. 1uL 6-8 mg/ml protein plus 1 uL well solution (18% PEG400, 0.2 M CaCl2, 0.1 M HEPES, pH7.2). Additive: 0.01 M L- ...Details: 3Xmolar excess of androstenol to purified mCAR LBD and incubate at RT for 1 h. 1uL 6-8 mg/ml protein plus 1 uL well solution (18% PEG400, 0.2 M CaCl2, 0.1 M HEPES, pH7.2). Additive: 0.01 M L-cysteine, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9792
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→29.55 Å / Num. all: 14394 / Num. obs: 14394 / Observed criterion σ(I): 0 / Biso Wilson estimate: 63.6 Å2

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.55 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 5492080.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1465 10.2 %RANDOM
Rwork0.229 ---
all0.2291 14394 --
obs0.2291 14394 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.6757 Å2 / ksol: 0.376432 e/Å3
Displacement parametersBiso mean: 43.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--5.87 Å20 Å2
3----5.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 40 33 3863
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.061.5
X-RAY DIFFRACTIONc_mcangle_it3.192
X-RAY DIFFRACTIONc_scbond_it5.392
X-RAY DIFFRACTIONc_scangle_it7.352.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 246 10.4 %
Rwork0.233 2117 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMATEN.TOP
X-RAY DIFFRACTION3ATEN.PARWATER.TOP

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