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- PDB-8aty: Crystal structure of PPAR gamma (PPARG) in complex with JP85 (com... -

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Basic information

Entry
Database: PDB / ID: 8aty
TitleCrystal structure of PPAR gamma (PPARG) in complex with JP85 (compound 1).
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsNUCLEAR PROTEIN / Nuclear receptor / PPARG / inhibitor / Structural Genomics / Structural Genomics Consortium / SGC
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 / arachidonate binding ...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 / 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 / positive regulation of fatty acid metabolic process / STAT family protein binding / response to lipid / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / negative regulation of SMAD protein signal transduction / lipid homeostasis / E-box binding / alpha-actinin binding / R-SMAD binding / negative regulation of vascular associated smooth muscle cell proliferation / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / white fat cell differentiation / negative regulation of macrophage derived foam cell differentiation / cellular response to low-density lipoprotein particle stimulus / negative regulation of lipid storage / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / cell fate commitment / negative regulation of osteoblast differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cell maturation / negative regulation of MAPK cascade / intracellular receptor signaling pathway / hormone-mediated signaling pathway / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / response to nutrient / epithelial cell differentiation / regulation of cellular response to insulin stimulus / peptide binding / negative regulation of miRNA transcription / negative regulation of angiogenesis / placenta development / Regulation of PTEN gene transcription / positive regulation of apoptotic signaling pathway / transcription coregulator binding / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / mRNA transcription by RNA polymerase II / negative regulation of transforming growth factor beta receptor signaling pathway / fatty acid metabolic process / PPARA activates gene expression / regulation of circadian rhythm / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / lipid metabolic process / positive regulation of miRNA transcription / regulation of blood pressure / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / nuclear receptor activity / cellular response to insulin stimulus / 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 / cellular response to hypoxia / DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / 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 / innate immune response / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II
Similarity search - Function
Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated 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. ...Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated 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
Similarity search - Domain/homology
Chem-O7O / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChaikuad, A. / Pollinger, J. / Merk, D. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Targeting the Alternative Vitamin E Metabolite Binding Site Enables Noncanonical PPAR gamma Modulation.
Authors: Arifi, S. / Marschner, J.A. / Pollinger, J. / Isigkeit, L. / Heitel, P. / Kaiser, A. / Obeser, L. / Hofner, G. / Proschak, E. / Knapp, S. / Chaikuad, A. / Heering, J. / Merk, D.
History
DepositionAug 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8288
Polymers31,6681
Non-polymers1,1607
Water2,792155
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-3 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.331, 65.331, 156.041
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 31667.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2 / References: UniProt: P37231
#2: Chemical ChemComp-O7O / 2-[4-chloranyl-6-(5,6,7,8-tetrahydronaphthalen-1-ylamino)pyrimidin-2-yl]sulfanylethanoic acid


Mass: 349.835 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H16ClN3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.4 M Ammonium sulfate, 0.1 M tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→44.3 Å / Num. obs: 27306 / % possible obs: 99.3 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.021 / Rrim(I) all: 0.065 / Net I/σ(I): 16.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.978.50.8772.226120.7670.3240.98798.5
7.36-44.38.10.02154510.0070.02295.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TSG

6tsg


Resolution: 1.9→44.3 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.834 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1319 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1353 5 %RANDOM
Rwork0.1755 ---
obs0.1768 25886 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 148.48 Å2 / Biso mean: 43.145 Å2 / Biso min: 23.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0 Å2
2--0.03 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.9→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 76 155 2427
Biso mean--52.15 46.22 -
Num. residues----277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132312
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172226
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.6443111
X-RAY DIFFRACTIONr_angle_other_deg1.3831.5965183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5845278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16124.327104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73515433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.098158
X-RAY DIFFRACTIONr_chiral_restr0.080.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022645
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02431
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 103 -
Rwork0.253 1887 -
all-1990 -
obs--99.6 %
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)
11.1691-1.0984-0.00672.0797-0.57270.5006-0.0312-0.09820.02280.27870.01050.0067-0.10560.02050.02070.1488-0.01610.02710.0921-0.01750.01217.559249.092871.0741
20.6896-0.0905-0.36361.2471-0.62221.0350.08170.1098-0.0491-0.08140.00110.1554-0.01-0.1052-0.08280.077-0.00540.00810.0746-0.01030.0308-1.317650.012961.473
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 363
2X-RAY DIFFRACTION2A364 - 477

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