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- PDB-5y2t: Structure of PPARgamma ligand binding domain - lobeglitazone complex -

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Basic information

Entry
Database: PDB / ID: 5y2t
TitleStructure of PPARgamma ligand binding domain - lobeglitazone complex
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / PPARgamma / nuclear receptor / pioglitazone / thiazolidinedione / ligand binding domain
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 / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / 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 / negative regulation of MAPK cascade / 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 / intracellular receptor signaling pathway / 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 / negative regulation of miRNA transcription / peptide binding / negative regulation of angiogenesis / transcription coregulator binding / positive regulation of apoptotic signaling pathway / Regulation of PTEN gene transcription / fatty acid metabolic process / placenta development / 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 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / regulation of blood pressure / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / 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 / DNA-binding transcription activator activity, RNA polymerase II-specific / double-stranded DNA binding / 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 / innate immune response / negative regulation of gene expression / 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 / : / 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
Chem-8LX / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsIm, Y.J. / Lee, M.
CitationJournal: Sci Rep / Year: 2017
Title: Structures of PPAR gamma complexed with lobeglitazone and pioglitazone reveal key determinants for the recognition of antidiabetic drugs
Authors: Lee, M.A. / Tan, L. / Yang, H. / Im, Y.G. / Im, Y.J.
History
DepositionJul 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7144
Polymers66,7532
Non-polymers9612
Water8,161453
1
A: Peroxisome proliferator-activated receptor gamma
hetero molecules

B: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7144
Polymers66,7532
Non-polymers9612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2100 Å2
ΔGint-9 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.267, 88.485, 57.999
Angle α, β, γ (deg.)90.00, 89.83, 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: 33376.625 Da / Num. of mol.: 2 / Fragment: UNP residues 235-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: modified pET28b
Details (production host): N-terminal cleavable His-tag fusion
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37231
#2: Chemical ChemComp-8LX / (5S)-5-[[4-[2-[[6-(4-methoxyphenoxy)pyrimidin-4-yl]-methyl-amino]ethoxy]phenyl]methyl]-1,3-thiazolidine-2,4-dione / Lobeglitazone


Mass: 480.536 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H24N4O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: agonist*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.16 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES NaOH pH7.5, 17.5% PEG 8000, 10% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 62190 / % possible obs: 99.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.038 / Net I/σ(I): 33.3
Reflection shellResolution: 1.7→1.735 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 3058 / Rpim(I) all: 0.178 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EMA

4ema


Resolution: 1.7→36.786 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.71
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 3148 5.06 %random
Rwork0.1922 ---
obs0.1938 62156 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.32 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4183 0 68 453 4704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174324
X-RAY DIFFRACTIONf_angle_d1.0185819
X-RAY DIFFRACTIONf_dihedral_angle_d16.3072686
X-RAY DIFFRACTIONf_chiral_restr0.202667
X-RAY DIFFRACTIONf_plane_restr0.006733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7002-1.72680.29641320.22452517X-RAY DIFFRACTION95
1.7268-1.75510.24841670.21762727X-RAY DIFFRACTION100
1.7551-1.78540.24811340.21322649X-RAY DIFFRACTION100
1.7854-1.81780.28791360.23082706X-RAY DIFFRACTION100
1.8178-1.85280.31251380.2222640X-RAY DIFFRACTION100
1.8528-1.89060.23431460.21522704X-RAY DIFFRACTION100
1.8906-1.93170.28371470.20942697X-RAY DIFFRACTION100
1.9317-1.97670.24211450.20872654X-RAY DIFFRACTION100
1.9767-2.02610.2761340.20572698X-RAY DIFFRACTION100
2.0261-2.08090.21031290.19522692X-RAY DIFFRACTION100
2.0809-2.14210.23621340.20272714X-RAY DIFFRACTION100
2.1421-2.21120.24261380.19482667X-RAY DIFFRACTION100
2.2112-2.29030.23631370.18972672X-RAY DIFFRACTION100
2.2903-2.38190.22911500.19292693X-RAY DIFFRACTION100
2.3819-2.49030.22711520.19752670X-RAY DIFFRACTION100
2.4903-2.62160.23861480.19942704X-RAY DIFFRACTION100
2.6216-2.78580.22081430.19792704X-RAY DIFFRACTION100
2.7858-3.00080.21381310.20092692X-RAY DIFFRACTION100
3.0008-3.30260.23021480.1972694X-RAY DIFFRACTION100
3.3026-3.78010.22211520.17952675X-RAY DIFFRACTION100
3.7801-4.76090.18131550.1652715X-RAY DIFFRACTION99
4.7609-36.79450.20531520.18682724X-RAY DIFFRACTION99

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