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- PDB-4s0s: STRUCTURE OF HUMAN PREGNANE X RECEPTOR LIGAND BINDING DOMAIN with... -

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Basic information

Entry
Database: PDB / ID: 4s0s
TitleSTRUCTURE OF HUMAN PREGNANE X RECEPTOR LIGAND BINDING DOMAIN with ADNECTIN-1
Components
  • Adnectin-1Monobody
  • Nuclear receptor subfamily 1 group I member 2
KeywordsIMMUNE SYSTEM / pregnane X receptor / PXR / ligand binding domain / steroid receptor coactivator-1 / CCR1 / Chemokine Receptor-1 / NR / nuclear receptor / AF / activation function / CYP / cytochrome P450 / MDR1 / multi-drug resistance gene-1
Function / homology
Function and homology information


xenobiotic transport / intermediate filament cytoskeleton / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / nuclear receptor activity ...xenobiotic transport / intermediate filament cytoskeleton / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / cell differentiation / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / 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 / zinc ion binding / nucleoplasm
Similarity search - Function
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 ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Nuclear receptor subfamily 1 group I member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKhan, J.A.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Developing Adnectins That Target SRC Co-Activator Binding to PXR: A Structural Approach toward Understanding Promiscuity of PXR.
Authors: Khan, J.A. / Camac, D.M. / Low, S. / Tebben, A.J. / Wensel, D.L. / Wright, M.C. / Su, J. / Jenny, V. / Gupta, R.D. / Ruzanov, M. / Russo, K.A. / Bell, A. / An, Y. / Bryson, J.W. / Gao, M. / ...Authors: Khan, J.A. / Camac, D.M. / Low, S. / Tebben, A.J. / Wensel, D.L. / Wright, M.C. / Su, J. / Jenny, V. / Gupta, R.D. / Ruzanov, M. / Russo, K.A. / Bell, A. / An, Y. / Bryson, J.W. / Gao, M. / Gambhire, P. / Baldwin, E.T. / Gardner, D. / Cavallaro, C.L. / Duncia, J.V. / Hynes, J.
History
DepositionJan 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor subfamily 1 group I member 2
B: Nuclear receptor subfamily 1 group I member 2
D: Adnectin-1
E: Adnectin-1


Theoretical massNumber of molelcules
Total (without water)98,9134
Polymers98,9134
Non-polymers00
Water0
1
A: Nuclear receptor subfamily 1 group I member 2
D: Adnectin-1


Theoretical massNumber of molelcules
Total (without water)49,4562
Polymers49,4562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-13 kcal/mol
Surface area17590 Å2
MethodPISA
2
B: Nuclear receptor subfamily 1 group I member 2
E: Adnectin-1


Theoretical massNumber of molelcules
Total (without water)49,4562
Polymers49,4562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-12 kcal/mol
Surface area17570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.234, 119.234, 83.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4

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Components

#1: Protein Nuclear receptor subfamily 1 group I member 2 / Orphan nuclear receptor PAR1 / Orphan nuclear receptor PXR / Pregnane X receptor / Steroid and ...Orphan nuclear receptor PAR1 / Orphan nuclear receptor PXR / Pregnane X receptor / Steroid and xenobiotic receptor / SXR


Mass: 36223.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR / Plasmid: pCO7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75469
#2: Protein Adnectin-1 / Monobody


Mass: 13232.593 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET9D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 7.0, 18%(V/V)1,6 hexanediol, and 3% (V/V) MPD. Crystals harvested next day using mother liquor supplemented with 21%(V/V) 1,6 hexanediol and 3%(V/V) MPD as cryoprotectant, ...Details: 0.1M HEPES pH 7.0, 18%(V/V)1,6 hexanediol, and 3% (V/V) MPD. Crystals harvested next day using mother liquor supplemented with 21%(V/V) 1,6 hexanediol and 3%(V/V) MPD as cryoprotectant, vapor diffusion, hanging drop, temperature 293K
PH range: 7.8?

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→48.56 Å / Num. obs: 29146 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 103.74 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 26
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.11.6refinement
PDB_EXTRACT3.15data extraction
BUSTERrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→34.91 Å / Cor.coef. Fo:Fc: 0.9327 / Cor.coef. Fo:Fc free: 0.9371 / SU R Cruickshank DPI: 0.557 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 1474 5.07 %RANDOM
Rwork0.2161 ---
obs0.2168 29083 99.98 %-
Displacement parametersBiso max: 195.05 Å2 / Biso mean: 92.93 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--11.1576 Å20 Å20 Å2
2---11.1576 Å20 Å2
3---22.3151 Å2
Refine analyzeLuzzati coordinate error obs: 0.444 Å
Refinement stepCycle: LAST / Resolution: 2.8→34.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5617 0 0 0 5617
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1882SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes125HARMONIC2
X-RAY DIFFRACTIONt_gen_planes841HARMONIC5
X-RAY DIFFRACTIONt_it5770HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion778SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6854SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5770HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7860HARMONIC21.16
X-RAY DIFFRACTIONt_omega_torsion4.41
X-RAY DIFFRACTIONt_other_torsion19.95
LS refinement shellResolution: 2.8→2.9 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2848 142 5 %
Rwork0.2657 2700 -
all0.2667 2842 -
obs--99.98 %

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