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- PDB-6fzg: PPAR gamma mutant complex -

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Basic information

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


prostaglandin receptor 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 / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / positive regulation of cholesterol transport / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of low-density lipoprotein receptor activity ...prostaglandin receptor 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 / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / positive regulation of cholesterol transport / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of low-density lipoprotein receptor activity / arachidonate binding / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / DNA binding domain binding / macrophage derived foam cell differentiation / 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 / 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 / alpha-actinin binding / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / white fat cell differentiation / negative regulation of BMP signaling pathway / cell fate commitment / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / negative regulation of MAPK cascade / BMP signaling pathway / retinoic acid receptor signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cell maturation / epithelial cell differentiation / negative regulation of signaling receptor activity / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / regulation of cellular response to insulin stimulus / negative regulation of angiogenesis / response to nutrient / negative regulation of miRNA transcription / Regulation of PTEN gene transcription / transcription coregulator binding / fatty acid metabolic process / negative regulation of smooth muscle cell proliferation / positive regulation of apoptotic signaling pathway / negative regulation of transforming growth factor beta receptor signaling pathway / peptide binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / regulation of circadian rhythm / placenta development / PPARA activates gene expression / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / positive regulation of miRNA transcription / regulation of blood pressure / cellular response to insulin stimulus / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / rhythmic process / glucose homeostasis / cellular response to hypoxia / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / intracellular membrane-bounded organelle / innate immune response / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression
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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-EDK / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1303
Polymers31,5991
Non-polymers5312
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-0 kcal/mol
Surface area13760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.375, 60.375, 162.174
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-700-

HOH

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Components

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


Mass: 31598.754 Da / Num. of mol.: 1 / Mutation: I290M
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: 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.: 1 / Source method: obtained synthetically / Formula: C30H29N3O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG 3350, 0.2 M NaCl, 0.1 M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.43 Å / Num. obs: 18330 / % possible obs: 100 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.07885 / Net I/σ(I): 18.02
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 0.5421 / % possible all: 100

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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: 2.1→48.426 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.97
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 711 3.88 %RANDOM
Rwork0.1641 ---
obs0.1658 18327 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→48.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 38 210 2466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062363
X-RAY DIFFRACTIONf_angle_d0.823199
X-RAY DIFFRACTIONf_dihedral_angle_d14.4371502
X-RAY DIFFRACTIONf_chiral_restr0.046363
X-RAY DIFFRACTIONf_plane_restr0.005439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.26220.28521380.19733425X-RAY DIFFRACTION100
2.2622-2.48980.25921400.17693450X-RAY DIFFRACTION100
2.4898-2.85010.25131410.17563495X-RAY DIFFRACTION100
2.8501-3.59060.22251410.17593510X-RAY DIFFRACTION100
3.5906-48.43880.17771510.15033736X-RAY DIFFRACTION100
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)
11.728-0.5266-0.46163.7885-0.56123.15120.21820.309-0.0426-0.5659-0.25850.12530.2345-0.2872-0.02940.5858-0.0554-0.02710.3188-0.04430.38797.0469102.626618.4169
22.232-0.16970.67681.5978-1.50852.2790.31050.7121-1.00030.17630.089-0.3256-0.1020.6714-0.31670.86280.2581-0.32331.118-0.13931.2456-12.3611121.34858.7791
31.9718-0.3596-0.12423.3956-0.87734.1760.07560.00030.0157-0.2464-0.03650.23940.043-0.7015-0.04870.3139-0.0519-0.02940.3602-0.03020.3321-0.4354109.414827.1558
43.7005-0.8016-0.24613.5830.62414.69540.1137-0.6861-0.15850.2237-0.0804-0.32990.59830.5383-0.08620.3755-0.0345-0.03450.2322-0.01840.313114.54397.084336.8908
55.7268-3.0710.84985.44390.16414.3886-0.1608-0.39910.89220.08380.0811-0.132-0.4549-0.65460.04610.3507-0.00950.01830.3974-0.02740.38552.1853115.929934.9342
64.17780.42021.03274.46410.21236.48960.2878-0.65330.5947-0.127-0.22250.995-1.0063-1.3521-0.02670.48020.0548-0.00320.849-0.12020.7968-13.8773113.705832.3348
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 202 through 258 )
2X-RAY DIFFRACTION2chain 'A' and (resid 259 through 272 )
3X-RAY DIFFRACTION3chain 'A' and (resid 273 through 402 )
4X-RAY DIFFRACTION4chain 'A' and (resid 403 through 430 )
5X-RAY DIFFRACTION5chain 'A' and (resid 431 through 459 )
6X-RAY DIFFRACTION6chain 'A' and (resid 460 through 477 )

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