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- PDB-6fzf: PPAR mutant complex -

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Basic information

Entry
Database: PDB / ID: 6fzf
TitlePPAR mutant complex
Components
  • Peroxisome proliferator-activated receptor gamma
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
KeywordsTRANSCRIPTION / nuclear receptor
Function / homology
Function and homology information


Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / cellular respiration / prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / 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 / Activation of PPARGC1A (PGC-1alpha) by phosphorylation ...Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / cellular respiration / prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / 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 / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / : / arachidonate binding / positive regulation of adiponectin secretion / negative regulation of cardiac muscle hypertrophy in response to stress / DNA binding domain binding / lipoprotein transport / positive regulation of vascular associated smooth muscle cell apoptotic process / WW domain binding / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / temperature homeostasis / lncRNA binding / response to muscle activity / negative regulation of SMAD protein signal transduction / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / response to starvation / lipid homeostasis / E-box binding / intracellular glucose homeostasis / alpha-actinin binding / negative regulation of vascular associated smooth muscle cell proliferation / fatty acid oxidation / R-SMAD binding / response to dietary excess / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / white fat cell differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / cell fate commitment / negative regulation of osteoblast differentiation / positive regulation of fat cell differentiation / negative regulation of MAPK cascade / adipose tissue development / BMP signaling pathway / long-chain fatty acid transport / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / nuclear retinoid X receptor binding / brown fat cell differentiation / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cell maturation / energy homeostasis / intracellular receptor signaling pathway / digestion / positive regulation of adipose tissue development / hormone-mediated signaling pathway / peroxisome proliferator activated receptor signaling pathway / epithelial cell differentiation / regulation of cellular response to insulin stimulus / response to nutrient / positive regulation of gluconeogenesis / negative regulation of miRNA transcription / peptide binding / RNA splicing / SUMOylation of transcription cofactors / negative regulation of angiogenesis / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / positive regulation of apoptotic signaling pathway / Regulation of PTEN gene transcription / nuclear receptor binding / respiratory electron transport chain / gluconeogenesis / fatty acid metabolic process / mitochondrion organization / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / placenta development / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / regulation of circadian rhythm / PML body / Nuclear Receptor transcription pathway / chromatin DNA binding
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 / : / Retinoid X Receptor / Retinoid X Receptor / RNA recognition motif ...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 / : / Retinoid X Receptor / Retinoid X 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-EDK / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRochel, N.
CitationJournal: Nat Commun / Year: 2019
Title: Recurrent activating mutations of PPAR gamma associated with luminal bladder tumors.
Authors: Rochel, N. / Krucker, C. / Coutos-Thevenot, L. / Osz, J. / Zhang, R. / Guyon, E. / Zita, W. / Vanthong, S. / Hernandez, O.A. / Bourguet, M. / Badawy, K.A. / Dufour, F. / Peluso-Iltis, C. / ...Authors: Rochel, N. / Krucker, C. / Coutos-Thevenot, L. / Osz, J. / Zhang, R. / Guyon, E. / Zita, W. / Vanthong, S. / Hernandez, O.A. / Bourguet, M. / Badawy, K.A. / Dufour, F. / Peluso-Iltis, C. / Heckler-Beji, S. / Dejaegere, A. / Kamoun, A. / de Reynies, A. / Neuzillet, Y. / Rebouissou, S. / Beraud, C. / Lang, H. / Massfelder, T. / Allory, Y. / Cianferani, S. / Stote, R.H. / Radvanyi, F. / Bernard-Pierrot, I.
History
DepositionMar 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
D: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8256
Polymers66,8344
Non-polymers9912
Water10,215567
1
A: Peroxisome proliferator-activated receptor gamma
C: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9133
Polymers33,4172
Non-polymers4961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-8 kcal/mol
Surface area13160 Å2
MethodPISA
2
B: Peroxisome proliferator-activated receptor gamma
D: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9133
Polymers33,4172
Non-polymers4961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-9 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.644, 123.684, 54.466
Angle α, β, γ (deg.)90.00, 95.31, 90.00
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: 31893.084 Da / Num. of mol.: 2 / Mutation: T475M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P37231
#2: Protein/peptide Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / PPARGC-1-alpha / Ligand effect modulator 6


Mass: 1523.854 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2
#3: Chemical ChemComp-EDK / (2~{S})-3-[4-[2-[methyl(pyridin-2-yl)amino]ethoxy]phenyl]-2-[[2-(phenylcarbonyl)phenyl]amino]propanoic acid


Mass: 495.569 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H29N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972422 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972422 Å / Relative weight: 1
ReflectionResolution: 1.95→17.626 Å / Num. obs: 50678 / % possible obs: 99 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.42
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.7533 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PRG

1prg


Resolution: 1.95→17.626 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.65
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 1539 3.04 %random
Rwork0.1522 ---
obs0.1534 50664 98.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→17.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4585 0 74 575 5234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074999
X-RAY DIFFRACTIONf_angle_d0.8456771
X-RAY DIFFRACTIONf_dihedral_angle_d15.2933189
X-RAY DIFFRACTIONf_chiral_restr0.046771
X-RAY DIFFRACTIONf_plane_restr0.005923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.01290.30361370.28314395X-RAY DIFFRACTION98
2.0129-2.08470.30591400.23714441X-RAY DIFFRACTION99
2.0847-2.1680.26531410.20524513X-RAY DIFFRACTION99
2.168-2.26650.26231390.19454443X-RAY DIFFRACTION99
2.2665-2.38570.21521400.17324446X-RAY DIFFRACTION99
2.3857-2.53480.21711400.17444487X-RAY DIFFRACTION99
2.5348-2.72980.23331410.17014500X-RAY DIFFRACTION99
2.7298-3.00330.21661400.1654458X-RAY DIFFRACTION98
3.0033-3.43510.20521390.15024440X-RAY DIFFRACTION98
3.4351-4.31740.15711400.11554454X-RAY DIFFRACTION98
4.3174-17.62650.14551420.12624548X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.78522.75584.68973.92632.11578.5691-0.30180.56840.1693-0.2690.25550.1172-0.35130.28890.10490.272-0.00170.03960.27330.01060.2296-17.557231.3671-23.4028
29.25750.8819-2.81967.038-0.6422.1188-0.0690.07951.04210.0475-0.07720.8939-0.4324-0.42520.13970.3127-0.0565-0.01770.335-0.03930.5658-7.814344.6601-0.9627
33.58730.03641.72061.5882-0.0053.8253-0.1311-0.9750.49440.80880.15190.1729-0.8184-0.70540.46660.54140.0708-0.03190.6-0.15230.6498-20.836842.34147.5577
42.88521.09581.891.40021.01823.5289-0.0097-0.14850.07620.0926-0.17470.18990.1586-0.28960.2170.2539-0.00270.0480.245-0.02340.2572-25.027427.7761-8.4959
52.45830.6307-0.45311.87121.7665.8170.0231-0.19040.10330.1456-0.0671-0.03250.24720.21720.04320.2173-0.00190.01510.25480.00570.2777-8.181829.8267-1.9784
67.73222.7604-2.7753.5057-0.97033.5254-0.1180.3389-0.44280.11340.0194-0.00620.1945-0.1720.14950.3102-0.01140.01880.1958-0.03080.2428-21.743820.0844-17.4577
76.24271.5251-2.11123.1981-0.3664.3413-0.50150.7088-0.9312-0.36770.1503-0.30670.5713-0.01550.31640.4170.02050.06070.253-0.06880.2667-17.55216.6895-26.2702
83.692-1.7874-3.8373.07343.20674.9022-0.4947-0.1697-0.45560.2932-0.1290.13061.5490.08430.62120.4319-0.02530.03570.23680.02510.2933-16.25817.3185-4.3765
99.71120.18515.49534.6085-1.56786.65950.0655-0.6725-0.1410.2353-0.44180.24360.6169-0.95410.46280.3414-0.08420.13720.41030.00590.3147-27.907724.88253.9677
106.56420.56570.13166.1261-4.34873.2370.0990.87760.1723-1.3828-0.04260.19950.61050.1469-0.03870.69070.0230.02180.3529-0.02180.2335-5.301-3.637-31.5191
117.97527.37120.09329.5128-3.80995.8743-0.33990.0967-0.3982-0.60650.18090.03020.5862-0.61840.16010.4342-0.0649-0.00120.2513-0.01090.3108-15.7666-14.3965-17.2745
128.5719-1.17622.11197.1159-2.77323.0097-0.0590.1222-0.5722-0.54680.0890.25740.63980.3466-0.01530.3833-0.0970.06170.31990.00480.442-19.4318-23.3049-3.7048
139.3809-0.4662-1.17137.2183-0.11725.6603-0.074-0.7346-0.18010.86020.25710.0590.1736-0.214-0.1550.41460.01840.06350.45390.09270.4402-6.0749-21.60445.5658
142.22040.3082-0.172.0366-0.79671.8779-0.0069-0.07980.01120.1239-0.03430.0224-0.11850.01740.03430.3282-0.00730.00610.1905-0.01870.2363-8.2137-5.635-9.1317
157.80670.51144.70272.8335-0.00665.4271-0.53380.46260.9488-0.72670.1920.4111-0.5185-0.06530.32990.5770.0267-0.0390.26710.05710.3522-9.85865.7266-26.508
162.947-1.11842.82124.1405-1.83223.3271-0.5668-0.33160.41011.06070.1085-0.0974-1.7583-0.22610.48290.54240.01980.02740.2545-0.0620.3316-10.30713.6941-4.2379
177.1394-0.2836-2.98227.40191.68312.25530.0991-1.19020.07660.9635-0.3565-0.3622-0.86640.61290.15650.5019-0.0547-0.0480.4382-0.00620.27951.1981-4.37222.8747
185.9499-3.17843.73694.7165-0.23733.37530.23990.4182-0.6118-0.34320.10910.5111-0.1155-0.8773-0.29920.2677-0.02940.05390.468-0.12880.4617-37.884829.1067-8.4248
193.6736-2.2539-1.83993.478-1.13043.63650.02270.2941-0.0988-0.0137-0.2797-0.64550.8691.07070.23240.35630.00850.01310.43390.06150.51111.0755-8.3494-9.9038
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 207 through 238 )
2X-RAY DIFFRACTION2chain 'A' and (resid 239 through 261 )
3X-RAY DIFFRACTION3chain 'A' and (resid 262 through 276 )
4X-RAY DIFFRACTION4chain 'A' and (resid 277 through 333 )
5X-RAY DIFFRACTION5chain 'A' and (resid 334 through 377 )
6X-RAY DIFFRACTION6chain 'A' and (resid 378 through 402 )
7X-RAY DIFFRACTION7chain 'A' and (resid 403 through 430 )
8X-RAY DIFFRACTION8chain 'A' and (resid 431 through 459 )
9X-RAY DIFFRACTION9chain 'A' and (resid 460 through 477 )
10X-RAY DIFFRACTION10chain 'B' and (resid 203 through 225 )
11X-RAY DIFFRACTION11chain 'B' and (resid 226 through 237 )
12X-RAY DIFFRACTION12chain 'B' and (resid 238 through 261 )
13X-RAY DIFFRACTION13chain 'B' and (resid 262 through 276 )
14X-RAY DIFFRACTION14chain 'B' and (resid 277 through 402 )
15X-RAY DIFFRACTION15chain 'B' and (resid 403 through 430 )
16X-RAY DIFFRACTION16chain 'B' and (resid 431 through 459 )
17X-RAY DIFFRACTION17chain 'B' and (resid 460 through 477 )
18X-RAY DIFFRACTION18chain 'C' and (resid 140 through 152 )
19X-RAY DIFFRACTION19chain 'D' and (resid 140 through 152 )

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