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- PDB-3ctb: Tethered PXR-LBD/SRC-1p apoprotein -

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Basic information

Entry
Database: PDB / ID: 3ctb
TitleTethered PXR-LBD/SRC-1p apoprotein
ComponentsPregnane X receptor, Linker, Steroid receptor coactivator 1
KeywordsTranscription / Transferase / pxr / src-1 / tethered / engineered / drug-drug interactions / DNA-binding / Metal-binding / Nucleus / Receptor / Transcription regulation / Zinc-finger
Function / homology
Function and homology information


labyrinthine layer morphogenesis / xenobiotic transport / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / intermediate filament cytoskeleton / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / steroid metabolic process ...labyrinthine layer morphogenesis / xenobiotic transport / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / intermediate filament cytoskeleton / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / steroid metabolic process / estrous cycle / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / xenobiotic catabolic process / nuclear retinoid X receptor binding / response to retinoic acid / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / xenobiotic metabolic process / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / response to progesterone / nuclear estrogen receptor binding / nuclear receptor binding / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / response to estradiol / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / cell differentiation / transcription coactivator activity / nuclear body / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
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 ...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 / PAS domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Nuclear receptor coactivator, interlocking / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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
Nuclear receptor subfamily 1 group I member 2 / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLesburg, C.A.
CitationJournal: Protein Eng.Des.Sel. / Year: 2008
Title: Construction and characterization of a fully active PXR/SRC-1 tethered protein with increased stability
Authors: Wang, W. / Prosise, W.W. / Chen, J. / Taremi, S.S. / Le, H.V. / Madison, V. / Cui, X. / Thomas, A. / Cheng, K.C. / Lesburg, C.A.
History
DepositionApr 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 2, 2014Group: Source and taxonomy
Revision 1.3Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pregnane X receptor, Linker, Steroid receptor coactivator 1
B: Pregnane X receptor, Linker, Steroid receptor coactivator 1


Theoretical massNumber of molelcules
Total (without water)78,3682
Polymers78,3682
Non-polymers00
Water6,413356
1
A: Pregnane X receptor, Linker, Steroid receptor coactivator 1


Theoretical massNumber of molelcules
Total (without water)39,1841
Polymers39,1841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pregnane X receptor, Linker, Steroid receptor coactivator 1


Theoretical massNumber of molelcules
Total (without water)39,1841
Polymers39,1841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-13.2 kcal/mol
Surface area27970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.240, 89.240, 105.230
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 Pregnane X receptor, Linker, Steroid receptor coactivator 1 / / Nuclear receptor subfamily 1 group I member 2 / Orphan nuclear receptor PXR / Orphan nuclear ...Nuclear receptor subfamily 1 group I member 2 / Orphan nuclear receptor PXR / Orphan nuclear receptor PAR1 / Steroid and xenobiotic receptor / SXR / NCoA-1 / Steroid receptor coactivator 1 / SRC-1 / RIP160 / Protein Hin-2 / Renal carcinoma antigen NY-REN-52


Mass: 39184.035 Da / Num. of mol.: 2
Fragment: PXR, residues 130-434, linker, SRC-1, residues 678-700
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: THE PEPTIDE FROM STEROID RECEPTOR COACTIVATOR 1 WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
Gene: NR1I2, PXR / Production host: Escherichia coli (E. coli)
References: UniProt: O75469, UniProt: Q15788, histone acetyltransferase
#2: Water ChemComp-HOH / water / Nuclear receptor coactivator 1 / NCoA-1 / SRC-1 / RIP160 / Protein Hin-2 / Renal carcinoma antigen NY-REN-52 / Water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 10-30% MPD or isopropanol, 100 mM imidazole, pH 7, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 26, 2005 / Details: VariMax HF
RadiationMonochromator: multilayer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 54259 / % possible obs: 98.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.58 % / Biso Wilson estimate: 44.07 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 13.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.49 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5082 / Rsym value: 0.461 / % possible all: 96.9

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Processing

Software
NameVersionClassification
BUSTER-TNT1.3.1refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1nrl

1nrl


Resolution: 2→45.31 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2713 5.01 %RANDOM
Rwork0.2044 ---
all0.2064 54906 --
obs0.2064 54169 98.5 %-
Displacement parametersBiso mean: 52.08 Å2
Baniso -1Baniso -2Baniso -3
1-2.0879694 Å20 Å20 Å2
2---1.58121524 Å20 Å2
3----0.50675416 Å2
Refine analyzeLuzzati coordinate error obs: 0.2555 Å
Refinement stepCycle: LAST / Resolution: 2→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4700 0 0 356 5056
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01148242
X-RAY DIFFRACTIONt_angle_deg1.14964672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg20.89110810
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_trig_c_planes0.011172
X-RAY DIFFRACTIONt_gen_planes0.0166855
X-RAY DIFFRACTIONt_it1.874482420
X-RAY DIFFRACTIONt_nbd0.068685
LS refinement shellResolution: 2→2.12 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2446 410 4.87 %
Rwork0.219 8014 -
all22.02 8424 -
obs--98.5 %

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