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- PDB-9f7x: Human PPARgamma ligand binding domain in complex with co-activato... -

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Basic information

Entry
Database: PDB / ID: 9f7x
TitleHuman PPARgamma ligand binding domain in complex with co-activator 1alpha peptide and bisphenol B (BPB)
Components
  • Peroxisome proliferator-activated receptor gamma
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
KeywordsTRANSCRIPTION / peroxisome proliferator-activated receptor gamma / bisphenol B / NUCLEAR PROTEIN
Function / homology
Function and homology information


Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / cellular respiration / MECP2 regulates transcription factors / beige fat cell differentiation / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly ...Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / cellular respiration / MECP2 regulates transcription factors / beige fat cell differentiation / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / arachidonate binding / positive regulation of adiponectin secretion / DNA binding domain binding / negative regulation of cardiac muscle hypertrophy in response to stress / positive regulation of vascular associated smooth muscle cell apoptotic process / response to starvation / positive regulation of fatty acid metabolic process / positive regulation of lipid metabolic process / STAT family protein binding / WW domain binding / response to muscle activity / response to lipid / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / LBD domain binding / lncRNA binding / temperature homeostasis / positive regulation of lipoprotein transport / response to dietary excess / fatty acid oxidation / negative regulation of SMAD protein signal transduction / lipid homeostasis / E-box binding / alpha-actinin binding / R-SMAD binding / negative regulation of blood vessel endothelial cell migration / white fat cell differentiation / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / positive regulation of cholesterol efflux / negative regulation of BMP signaling pathway / monocyte differentiation / adipose tissue development / cell fate commitment / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cellular response to low-density lipoprotein particle stimulus / negative regulation of mitochondrial fission / BMP signaling pathway / long-chain fatty acid transport / negative regulation of osteoblast differentiation / positive regulation of fat cell differentiation / nuclear retinoid X receptor binding / fat cell differentiation / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / digestion / intracellular receptor signaling pathway / energy homeostasis / negative regulation of MAPK cascade / cell maturation / peptide binding / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / regulation of cellular response to insulin stimulus / positive regulation of adipose tissue development / response to nutrient / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / SUMOylation of transcription cofactors / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / positive regulation of gluconeogenesis / negative regulation of miRNA transcription / intracellular glucose homeostasis / RNA splicing / brown fat cell differentiation / negative regulation of angiogenesis / placenta development / Regulation of PTEN gene transcription / nuclear receptor binding / transcription coregulator binding / gluconeogenesis / positive regulation of apoptotic signaling pathway / respiratory electron transport chain / SUMOylation of intracellular receptors / transcription coregulator activity / circadian regulation of gene expression / negative regulation of smooth muscle cell proliferation / transcription initiation at RNA polymerase II promoter / mitochondrion organization / Heme signaling / negative regulation of transforming growth factor beta receptor signaling pathway / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / fatty acid metabolic process / regulation of circadian rhythm / Transcriptional regulation of white adipocyte differentiation
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 / Double treble clef zinc finger, C4 type / 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
bisphenol-B / 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: 1.63 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)34,7223
Polymers34,4802
Non-polymers2421
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-8 kcal/mol
Surface area13750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.358, 54.615, 66.722
Angle α, β, γ (deg.)90.000, 93.600, 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-H3W / bisphenol-B


Mass: 242.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20% w/v PEG 3350, 0.337 M 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: 0.9755 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: 0.9755 Å / Relative weight: 1
ReflectionResolution: 1.63→42.23 Å / Num. obs: 28352 / % possible obs: 98.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 17.89 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.3
Reflection shellResolution: 1.63→1.8 Å / Num. unique obs: 731 / CC1/2: 0.437

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Processing

Software
NameVersionClassification
STARANISOdata scaling
PHENIX1.20.1_4487refinement
XDSdata reduction
PDB_EXTRACTdata extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.63→42.23 Å / SU ML: 0.2632 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.2329
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2899 4042 14.26 %
Rwork0.2493 24310 -
obs0.2553 28352 40.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.75 Å2
Refinement stepCycle: LAST / Resolution: 1.63→42.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 18 115 2336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00352282
X-RAY DIFFRACTIONf_angle_d0.53063077
X-RAY DIFFRACTIONf_chiral_restr0.0354356
X-RAY DIFFRACTIONf_plane_restr0.0038400
X-RAY DIFFRACTIONf_dihedral_angle_d13.4417888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.650.286480.40834X-RAY DIFFRACTION1.76
1.65-1.670.283790.35560X-RAY DIFFRACTION2.82
1.67-1.690.3715180.3102127X-RAY DIFFRACTION6.22
1.69-1.710.289240.3528156X-RAY DIFFRACTION7.65
1.72-1.740.3076380.3855192X-RAY DIFFRACTION9.6
1.74-1.760.2884560.3464240X-RAY DIFFRACTION12.2
1.76-1.790.289420.2963316X-RAY DIFFRACTION14.78
1.79-1.820.3026630.3093368X-RAY DIFFRACTION18.01
1.82-1.850.3233670.3401438X-RAY DIFFRACTION20.32
1.85-1.880.3595630.3213491X-RAY DIFFRACTION22.95
1.88-1.910.4062720.3221530X-RAY DIFFRACTION24.68
1.91-1.950.3056700.3389617X-RAY DIFFRACTION27.9
1.95-1.990.3914660.3086632X-RAY DIFFRACTION29.03
1.99-2.030.28651160.2822695X-RAY DIFFRACTION33.39
2.03-2.080.33561390.2916679X-RAY DIFFRACTION33.91
2.08-2.130.34881470.2872736X-RAY DIFFRACTION36.11
2.13-2.190.35361460.2938839X-RAY DIFFRACTION40.72
2.19-2.250.32831470.2874897X-RAY DIFFRACTION42.25
2.25-2.330.32271720.2782952X-RAY DIFFRACTION46.66
2.33-2.410.28531610.27891063X-RAY DIFFRACTION50.33
2.41-2.510.30931680.28331100X-RAY DIFFRACTION51.67
2.51-2.620.31871970.29021182X-RAY DIFFRACTION56.91
2.62-2.760.31522390.26831195X-RAY DIFFRACTION59.53
2.76-2.930.27932400.26911386X-RAY DIFFRACTION66.69
2.93-3.160.29653020.25531467X-RAY DIFFRACTION72.41
3.16-3.480.29273440.25641687X-RAY DIFFRACTION83.61
3.48-3.980.26533250.21772024X-RAY DIFFRACTION96.19
3.98-5.010.24292620.20422154X-RAY DIFFRACTION99.1
5.01-42.230.27343410.22142053X-RAY DIFFRACTION97.91
Refinement TLS params.Method: refined / Origin x: 6.90489524009 Å / Origin y: 9.11803984357 Å / Origin z: 17.4129505222 Å
111213212223313233
T-0.0994931464479 Å20.0252189633426 Å20.0545082243352 Å2--0.0647429679322 Å2-0.0420729689411 Å2--0.0154014247258 Å2
L0.450741121063 °2-0.116849885927 °20.147856282215 °2-0.524005620649 °2-0.226626801782 °2--0.442973551534 °2
S0.0847176296609 Å °0.430906915875 Å °0.0856857545167 Å °0.152682627653 Å °-0.111772197038 Å °-0.382190142308 Å °-0.138596163248 Å °0.495512767476 Å °-0.0876927517607 Å °
Refinement TLS groupSelection details: all

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