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- PDB-8bf1: High-resolution structure of unliganded PPAR gamma in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8bf1
TitleHigh-resolution structure of unliganded PPAR gamma in complex with the peptide PGC-1 alpha
Components
  • Peroxisome proliferator-activated receptor gamma
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
KeywordsNUCLEAR PROTEIN / PPAR gamma activation / co-activator peptide / ligand binding domain / nuclear receptor
Function / homology
Function and homology information


Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / fatty acid oxidation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / prostaglandin receptor activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / cellular respiration / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly ...Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / fatty acid oxidation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / prostaglandin receptor activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / cellular respiration / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / beige fat cell differentiation / negative regulation of vascular endothelial cell proliferation / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / arachidonate binding / positive regulation of adiponectin secretion / white fat cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / DNA binding domain binding / negative regulation of cardiac muscle hypertrophy in response to stress / response to muscle activity / positive regulation of lipid metabolic process / response to starvation / STAT family protein binding / positive regulation of fatty acid metabolic process / WW domain binding / negative regulation of type II interferon-mediated signaling pathway / energy homeostasis / adipose tissue development / LBD domain binding / negative regulation of cholesterol storage / temperature homeostasis / response to lipid / cell fate commitment / positive regulation of lipoprotein transport / lipid homeostasis / negative regulation of SMAD protein signal transduction / cell maturation / E-box binding / lncRNA binding / R-SMAD binding / brown fat cell differentiation / negative regulation of BMP signaling pathway / negative regulation of blood vessel endothelial cell migration / monocyte differentiation / negative regulation of vascular associated smooth muscle cell proliferation / alpha-actinin binding / negative regulation of macrophage derived foam cell differentiation / BMP signaling pathway / negative regulation of lipid storage / positive regulation of cholesterol efflux / positive regulation of fat cell differentiation / cellular response to low-density lipoprotein particle stimulus / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / fat cell differentiation / long-chain fatty acid transport / negative regulation of osteoblast differentiation / placenta development / nuclear retinoid X receptor binding / retinoic acid receptor signaling pathway / negative regulation of mitochondrial fission / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / digestion / hormone-mediated signaling pathway / positive regulation of gluconeogenesis / intracellular receptor signaling pathway / negative regulation of MAPK cascade / peroxisome proliferator activated receptor signaling pathway / positive regulation of adipose tissue development / gluconeogenesis / peptide binding / negative regulation of angiogenesis / epithelial cell differentiation / response to nutrient / regulation of cellular response to insulin stimulus / positive regulation of apoptotic signaling pathway / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / SUMOylation of transcription cofactors / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / fatty acid metabolic process / negative regulation of miRNA transcription / RNA splicing / intracellular glucose homeostasis / negative regulation of transforming growth factor beta receptor signaling pathway / nuclear receptor binding / Regulation of PTEN gene transcription / transcription coregulator binding / negative regulation of smooth muscle cell proliferation / mitochondrion organization / SUMOylation of intracellular receptors / circadian regulation of gene expression / respiratory electron transport chain / RNA polymerase II transcription regulator complex / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / transcription initiation at RNA polymerase II promoter / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway
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
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: 1.36 Å
AuthorsUseini, A. / Straeter, N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)Sfb1052-Z6 Germany
CitationJournal: Environ Int / Year: 2023
Title: Structural basis of the activation of PPAR gamma by the plasticizer metabolites MEHP and MINCH.
Authors: Useini, A. / Engelberger, F. / Kunze, G. / Strater, N.
History
DepositionOct 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)34,4802
Polymers34,4802
Non-polymers00
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-9 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.706, 54.209, 66.089
Angle α, β, γ (deg.)90.000, 106.730, 90.000
Int Tables number4
Space group name H-MP1211

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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) / Strain (production host): BL(DE3)21 / 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: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARGC1A, LEM6, PGC1, PGC1A, PPARGC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBK2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH 6.5 0.2 M ammonium acetate 0.01 M gunidine hydrochloride

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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: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.36→63.29 Å / Num. obs: 60971 / % possible obs: 96.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 17.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.029 / Rrim(I) all: 0.076 / Net I/σ(I): 12.4 / Num. measured all: 388613 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.36-1.392.10.871284313400.4190.7281.143143.2
7.47-63.295.60.05822203990.9910.0280.0652895.4

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6MS7

6ms7


Resolution: 1.36→41.17 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1811 2394 3.93 %
Rwork0.1677 58536 -
obs0.1682 60930 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.69 Å2 / Biso mean: 34.7213 Å2 / Biso min: 10.93 Å2
Refinement stepCycle: final / Resolution: 1.36→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 0 271 2449
Biso mean---36.29 -
Num. residues----273
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.36-1.390.3549630.34031714177748
1.39-1.420.32321380.2763390352895
1.42-1.450.23181430.226535603703100
1.45-1.490.21191420.204934983640100
1.49-1.530.21861400.193235303670100
1.53-1.580.2131670.195435683735100
1.58-1.630.22381290.180235533682100
1.63-1.690.18931540.172235623716100
1.69-1.750.1821450.168835333678100
1.75-1.830.17991480.16435743722100
1.83-1.930.17551510.175235333684100
1.93-2.050.18671650.165435443709100
2.05-2.210.15291310.148935733704100
2.21-2.430.16761340.147335973731100
2.43-2.780.16911460.155935603706100
2.78-3.510.18681550.165735903745100
3.51-41.170.16791430.16583657380099

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