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- PDB-9f7w: Humman PPARgamma ligand binding domain in complex with co-activat... -

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Basic information

Entry
Database: PDB / ID: 9f7w
TitleHumman PPARgamma ligand binding domain in complex with co-activator 1alpha peptide and bisphenol A (BPA)
Components
  • Peroxisome proliferator-activated receptor gamma
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
KeywordsTRANSCRIPTION / peroxisome proliferator-activated receptor gamma / bisphenol A / NUCLEAR PROTEIN
Function / homology
Function and homology information


: / positive regulation of fatty acid oxidation / prostaglandin receptor activity / regulation of cholesterol transporter activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / lncRNA binding / response to muscle activity / negative regulation of extracellular matrix assembly ...: / positive regulation of fatty acid oxidation / prostaglandin receptor activity / regulation of cholesterol transporter activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / lncRNA binding / response to muscle activity / negative regulation of extracellular matrix assembly / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration / negative regulation of vascular endothelial cell proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonic acid binding / positive regulation of low-density lipoprotein receptor activity / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / DNA binding domain binding / macrophage derived foam cell differentiation / temperature homeostasis / STAT family protein binding / positive regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / LBD domain binding / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / E-box binding / intracellular glucose homeostasis / response to starvation / alpha-actinin binding / fatty acid oxidation / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / response to dietary excess / negative regulation of macrophage derived foam cell differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / white fat cell differentiation / negative regulation of BMP signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / negative regulation of mitochondrial fission / positive regulation of cholesterol efflux / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / retinoic acid receptor signaling pathway / cell fate commitment / adipose tissue development / BMP signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / long-chain fatty acid transport / brown fat cell differentiation / energy homeostasis / nuclear retinoid X receptor binding / cell maturation / positive regulation of gluconeogenesis / negative regulation of signaling receptor activity / digestion / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / hormone-mediated signaling pathway / respiratory electron transport chain / negative regulation of angiogenesis / RNA splicing / response to nutrient / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / mitochondrion organization / nuclear receptor coactivator activity / negative regulation of MAP kinase activity / fatty acid metabolic process / Regulation of PTEN gene transcription / transcription coregulator binding / gluconeogenesis / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / peptide binding / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / placenta development / regulation of circadian rhythm / lipid metabolic process / PPARA activates gene expression / chromatin DNA binding / PML body
Similarity search - Function
PGC-1alpha, RNA recognition motif / PGC-1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / : / Peroxisome proliferator-activated receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...PGC-1alpha, RNA recognition motif / PGC-1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / : / Peroxisome proliferator-activated receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / 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 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
4,4'-PROPANE-2,2-DIYLDIPHENOL / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.25 Å
AuthorsUseini, A. / Strater, N.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)209933838 Germany
German Research Foundation (DFG)421152132 Germany
CitationJournal: Biomolecules / Year: 2024
Title: Structural Studies on the Binding Mode of Bisphenols to PPAR gamma.
Authors: Useini, A. / Schwerin, I.K. / Kunze, G. / Strater, N.
History
DepositionMay 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor gamma
B: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9374
Polymers34,4802
Non-polymers4572
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-3 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.800, 54.190, 66.472
Angle α, β, γ (deg.)90.000, 107.030, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Peroxisome proliferator-activated receptor gamma / PPAR-gamma / Nuclear receptor subfamily 1 group C member 3


Mass: 32412.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli (E. coli) / References: UniProt: P37231
#2: Protein/peptide Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / PGC-1-alpha / PPAR-gamma coactivator 1-alpha / PPARGC-1-alpha / Ligand effect modulator 6


Mass: 2067.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2
#3: Chemical ChemComp-2OH / 4,4'-PROPANE-2,2-DIYLDIPHENOL / 4,4'-ISOPROPYLIDENEDIPHENOL / BISPHENOL A


Mass: 228.286 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H16O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20% w/v PEG 3350, 0.2 M magnesium acetate, 137 mM sodium chloride, 8.1 mM disodium hydrogen phosphate, 1.5 mM potassium dihydrogen phosphate, 2.7 mM potassium chloride, 1 mM peptide, 15 mM BPB, 1.5 % DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.25→41.88 Å / Num. obs: 118830 / % possible obs: 98.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 16.96 Å2 / CC1/2: 0.99 / Net I/σ(I): 12.8
Reflection shellResolution: 1.25→1.36 Å / Num. unique obs: 3027 / CC1/2: 0.615 / % possible all: 99

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Processing

Software
NameVersionClassification
STARANISOdata scaling
PHENIX1.20.1_4487refinement
XDSdata reduction
PDB_EXTRACTdata extraction
Cootmodel building
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.25→41.88 Å / SU ML: 0.1249 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9806
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1889 5612 4.72 %
Rwork0.1622 113218 -
obs0.1634 118830 74.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.77 Å2
Refinement stepCycle: LAST / Resolution: 1.25→41.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2265 0 34 325 2624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792391
X-RAY DIFFRACTIONf_angle_d0.90473241
X-RAY DIFFRACTIONf_chiral_restr0.0623375
X-RAY DIFFRACTIONf_plane_restr0.0081438
X-RAY DIFFRACTIONf_dihedral_angle_d13.9638949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.4057160.2613182X-RAY DIFFRACTION3.66
1.27-1.280.2517180.2812346X-RAY DIFFRACTION6.83
1.28-1.30.2744180.2788556X-RAY DIFFRACTION10.87
1.3-1.310.253280.3084738X-RAY DIFFRACTION14.46
1.31-1.330.3047580.27121006X-RAY DIFFRACTION19.9
1.33-1.350.2467680.28391297X-RAY DIFFRACTION25.92
1.35-1.370.2461960.27971760X-RAY DIFFRACTION34.35
1.37-1.390.29481280.26472297X-RAY DIFFRACTION45.58
1.39-1.410.25981250.27952862X-RAY DIFFRACTION55.25
1.41-1.430.29621640.29093506X-RAY DIFFRACTION69.85
1.43-1.460.28791970.2724011X-RAY DIFFRACTION78.33
1.46-1.490.25471900.25114462X-RAY DIFFRACTION87.1
1.49-1.510.26362510.23094805X-RAY DIFFRACTION92.58
1.51-1.550.23792830.22044865X-RAY DIFFRACTION97.3
1.55-1.580.22832880.21244975X-RAY DIFFRACTION98.06
1.58-1.620.2392550.19985031X-RAY DIFFRACTION98.88
1.62-1.660.21472460.19184979X-RAY DIFFRACTION98.42
1.66-1.70.19342260.19165070X-RAY DIFFRACTION98.42
1.7-1.750.19452730.18995008X-RAY DIFFRACTION97.98
1.75-1.810.22152470.18524963X-RAY DIFFRACTION98.92
1.81-1.870.20892880.17925045X-RAY DIFFRACTION98.89
1.87-1.950.19412460.17045054X-RAY DIFFRACTION99.05
1.95-2.040.17742360.15314989X-RAY DIFFRACTION98.88
2.04-2.140.17932290.14735058X-RAY DIFFRACTION98.14
2.14-2.280.17432330.13975040X-RAY DIFFRACTION99
2.28-2.450.15022420.13155086X-RAY DIFFRACTION99.02
2.45-2.70.16492300.13955048X-RAY DIFFRACTION98.88
2.7-3.090.16652550.15325021X-RAY DIFFRACTION98.62
3.09-3.890.18392450.14065085X-RAY DIFFRACTION99.29
3.89-41.880.17952330.15315073X-RAY DIFFRACTION99.4
Refinement TLS params.Method: refined / Origin x: 46.3993467444 Å / Origin y: 10.0579499634 Å / Origin z: 18.5375479032 Å
111213212223313233
T0.133440929889 Å20.00658539242419 Å2-0.00182808126711 Å2-0.133478707037 Å2-0.00464547578403 Å2--0.120943523064 Å2
L0.516012710088 °20.125419689536 °2-0.114541513322 °2-0.666926582282 °20.0212777573315 °2--0.490360861149 °2
S-0.00283468493823 Å °0.0768651850553 Å °-0.0230013144509 Å °-0.136738671324 Å °0.00987756691422 Å °-0.0363272656531 Å °0.0328957828525 Å °0.0186892640984 Å °-1.04898277619E-5 Å °
Refinement TLS groupSelection details: all

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