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- PDB-6fzy: PPAR mutant -

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Basic information

Entry
Database: PDB / ID: 6fzy
TitlePPAR mutant
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / nuclear receptor
Function / homology
Function and homology information


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 / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / : ...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 / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / : / arachidonate binding / positive regulation of adiponectin secretion / negative regulation of triglyceride storage / DNA binding domain binding / lipoprotein transport / positive regulation of vascular associated smooth muscle cell apoptotic process / STAT family protein binding / WW domain binding / 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 / lipid homeostasis / E-box binding / alpha-actinin binding / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / 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 / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / negative regulation of MAPK cascade / retinoic acid receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cell maturation / negative regulation of signaling receptor activity / positive regulation of adipose tissue development / hormone-mediated signaling pathway / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / response to nutrient / regulation of cellular response to insulin stimulus / negative regulation of miRNA transcription / peptide binding / negative regulation of angiogenesis / transcription coregulator binding / Regulation of PTEN gene transcription / fatty acid metabolic process / placenta development / positive regulation of apoptotic signaling pathway / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / mRNA transcription by RNA polymerase II / PPARA activates gene expression / regulation of circadian rhythm / lipid metabolic process / regulation of blood pressure / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / nuclear receptor activity / rhythmic process / glucose homeostasis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / cellular response to hypoxia / sequence-specific DNA binding / nucleic acid binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / receptor complex / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / intracellular membrane-bounded organelle / innate immune response / negative regulation of DNA-templated transcription / positive regulation of gene expression / chromatin binding
Similarity search - Function
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 / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 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 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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


Theoretical massNumber of molelcules
Total (without water)63,7862
Polymers63,7862
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-8 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.190, 62.670, 165.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.5 M ammonium sulfate, 0.1 M PIPES pH7, 0.9 M disodium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972422 Å
DetectorType: DECTRIS PILATUS3 S 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: 3.1→44.144 Å / Num. obs: 12300 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 113.38 Å2 / Rmerge(I) obs: 0.08036 / Net I/σ(I): 16.78
Reflection shellResolution: 3.1→3.211 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 3.1→42.65 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2348 --
Rwork0.195 --
obs0.195 12293 99.86 %
Refinement stepCycle: LAST / Resolution: 3.1→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4260 0 0 47 4307

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