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- PDB-6tsg: Crystal structure of Peroxisome proliferator-activated receptor g... -

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Basic information

Entry
Database: PDB / ID: 6tsg
TitleCrystal structure of Peroxisome proliferator-activated receptor gamma (PPARG) in complex with TETRAC
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsDNA BINDING PROTEIN / PPARg / steroid hormone receptor / inhibitor / Structural Genomics / Structural Genomics Consortium / SGC
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 / 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 / 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 / cellular response to low-density lipoprotein particle stimulus / negative regulation of lipid storage / white fat cell differentiation / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / cell fate commitment / 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 / negative regulation of signaling receptor activity / epithelial cell differentiation / 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 / positive regulation of apoptotic signaling pathway / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / peptide binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / placenta development / regulation of circadian rhythm / PPARA activates gene expression / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / negative regulation of inflammatory response / regulation of blood pressure / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / 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 / : / 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. ...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 / 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
Similarity search - Domain/homology
3,3',5,5'-TETRAIODOTHYROACETIC ACID / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsChaikuad, A. / Gellrich, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Merk, D. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2020
Title: l-Thyroxin and the Nonclassical Thyroid Hormone TETRAC Are Potent Activators of PPAR gamma.
Authors: Gellrich, L. / Heitel, P. / Heering, J. / Kilu, W. / Pollinger, J. / Goebel, T. / Kahnt, A. / Arifi, S. / Pogoda, W. / Paulke, A. / Steinhilber, D. / Proschak, E. / Wurglics, M. / Schubert- ...Authors: Gellrich, L. / Heitel, P. / Heering, J. / Kilu, W. / Pollinger, J. / Goebel, T. / Kahnt, A. / Arifi, S. / Pogoda, W. / Paulke, A. / Steinhilber, D. / Proschak, E. / Wurglics, M. / Schubert-Zsilavecz, M. / Chaikuad, A. / Knapp, S. / Bischoff, I. / Furst, R. / Merk, D.
History
DepositionDec 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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)32,4162
Polymers31,6681
Non-polymers7481
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint0 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.678, 61.678, 166.487
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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-T4A / 3,3',5,5'-TETRAIODOTHYROACETIC ACID


Mass: 747.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8I4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 33% PEG 3350 and 0.15 M sodium citrate

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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 EIGER X 16M / 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: 2.98→41.62 Å / Num. obs: 7082 / % possible obs: 99.3 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.038 / Rrim(I) all: 0.099 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.98-3.146.70.9721.810140.6080.4291.13799.9
9.43-41.625.10.02227010.010.02595.1

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6avi

6avi


Resolution: 2.98→41.62 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.897 / SU B: 48.477 / SU ML: 0.417 / SU R Cruickshank DPI: 0.4339 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.497
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2924 356 5.1 %RANDOM
Rwork0.2365 ---
obs0.2395 6675 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 213.06 Å2 / Biso mean: 103.512 Å2 / Biso min: 50.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å2-0 Å2-0 Å2
2--1.72 Å2-0 Å2
3----3.44 Å2
Refinement stepCycle: final / Resolution: 2.98→41.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2057 0 22 4 2083
Biso mean--118.69 63.06 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132114
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172032
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.6352853
X-RAY DIFFRACTIONr_angle_other_deg1.1481.584728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8335256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08524.257101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84515402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.21158
X-RAY DIFFRACTIONr_chiral_restr0.0530.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022369
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02399
LS refinement shellResolution: 2.981→3.058 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 19 -
Rwork0.344 482 -
all-501 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -10.0264 Å / Origin y: 1.8412 Å / Origin z: -27.0149 Å
111213212223313233
T0.2487 Å2-0.0153 Å20.0251 Å2-0.0271 Å2-0.0059 Å2--0.258 Å2
L5.182 °2-0.3996 °21.6733 °2-1.3271 °2-0.2829 °2--3.4401 °2
S0.1063 Å °0.0222 Å °-1.1076 Å °-0.0211 Å °0.0597 Å °-0.0299 Å °0.8162 Å °0.0495 Å °-0.166 Å °

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