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- PDB-5lsg: PPARgamma complex with the betulinic acid -

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Basic information

Entry
Database: PDB / ID: 5lsg
TitlePPARgamma complex with the betulinic acid
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsSIGNALING PROTEIN / Antagonist / Complex / Transcription Factor / 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
Betulinic Acid / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPochetti, G. / Montanari, R. / Capelli, D. / Loiodice, F. / Laghezza, A. / Calleri, E. / Paiardini, A.
CitationJournal: Sci Rep / Year: 2017
Title: Betulinic acid is a PPAR gamma antagonist that improves glucose uptake, promotes osteogenesis and inhibits adipogenesis.
Authors: Brusotti, G. / Montanari, R. / Capelli, D. / Cattaneo, G. / Laghezza, A. / Tortorella, P. / Loiodice, F. / Peiretti, F. / Bonardo, B. / Paiardini, A. / Calleri, E. / Pochetti, G.
History
DepositionAug 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)69,6203
Polymers69,1662
Non-polymers4551
Water2,540141
1
A: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0382
Polymers34,5831
Non-polymers4551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxisome proliferator-activated receptor gamma


Theoretical massNumber of molelcules
Total (without water)34,5831
Polymers34,5831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.860, 60.850, 118.030
Angle α, β, γ (deg.)90.00, 102.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 34582.906 Da / Num. of mol.: 2 / Fragment: UNP residues 223-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37231
#2: Chemical ChemComp-QZQ / Betulinic Acid


Mass: 454.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H46O3 / Comment: anticancer, antiinflammatory, antiretroviral*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: reservoir: 0.8M NACITRATE, 0.15M TRIS, PH8.0. The crystals were soaked for one week in a storage solution (1.2 M Na Citrate, 0.15M Tris, pH 8.0) containing the ligand BA (0.5 mM).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 30, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 43045 / % possible obs: 98.5 % / Redundancy: 5.28 % / CC1/2: 1 / Rmerge(I) obs: 0.03 / Net I/σ(I): 29.25
Reflection shellResolution: 2→2.2 Å / Redundancy: 5.32 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 3.74 / CC1/2: 0.924 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D6D

3d6d


Resolution: 2→45.683 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 2153 5 %
Rwork0.2266 --
obs0.2286 43025 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→45.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4121 0 33 141 4295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094215
X-RAY DIFFRACTIONf_angle_d1.2655696
X-RAY DIFFRACTIONf_dihedral_angle_d16.1771592
X-RAY DIFFRACTIONf_chiral_restr0.05669
X-RAY DIFFRACTIONf_plane_restr0.006714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.04660.3731410.34322662X-RAY DIFFRACTION96
2.0466-2.09780.33551410.30762682X-RAY DIFFRACTION98
2.0978-2.15450.3191420.27512703X-RAY DIFFRACTION98
2.1545-2.21790.30481430.26812722X-RAY DIFFRACTION99
2.2179-2.28950.29361420.26642695X-RAY DIFFRACTION99
2.2895-2.37130.29761430.24882713X-RAY DIFFRACTION99
2.3713-2.46620.31081430.25062714X-RAY DIFFRACTION99
2.4662-2.57850.28031440.24732720X-RAY DIFFRACTION99
2.5785-2.71440.29771430.24482723X-RAY DIFFRACTION99
2.7144-2.88440.33571450.24352760X-RAY DIFFRACTION99
2.8844-3.10710.27761460.24852762X-RAY DIFFRACTION99
3.1071-3.41970.2471440.23442747X-RAY DIFFRACTION99
3.4197-3.91430.25141460.20762761X-RAY DIFFRACTION100
3.9143-4.93070.24541460.1912782X-RAY DIFFRACTION100
4.9307-45.6950.22491440.21422726X-RAY DIFFRACTION95

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