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- PDB-9l3t: PPARgamma Ligand binding domain in complex with piperine -

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Basic information

Entry
Database: PDB / ID: 9l3t
TitlePPARgamma Ligand binding domain in complex with piperine
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / PPARgamma / piperine / nuclear receptor / nutural product / Peroxisome Proliferator-Activated Receptor / transcription factor / ligand binding domain / NUCLEAR PROTEIN
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 / DNA binding domain binding / negative regulation of cardiac muscle hypertrophy in response to stress / 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 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 / 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 / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / positive regulation of cholesterol efflux / negative regulation of BMP signaling pathway / 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 / response to nutrient / peroxisome proliferator activated receptor signaling pathway / 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 / negative regulation of smooth muscle cell proliferation / SUMOylation of intracellular receptors / negative regulation of transforming growth factor beta receptor signaling pathway / mRNA transcription by RNA polymerase II / fatty acid metabolic process / PPARA activates gene expression / regulation of circadian rhythm / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / 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 / 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 / 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 / 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 / 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-AYR / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsEgawa, D. / Ishida, H. / Katakawa, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Molecular interactions between piperine and peroxisome proliferator-activated receptor gamma ligand-binding domain revealed using co-crystallization studies.
Authors: Egawa, D. / Ishida, H. / Katakawa, K.
History
DepositionDec 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)63,1843
Polymers62,8992
Non-polymers2851
Water64936
1
A: Peroxisome proliferator-activated receptor gamma
hetero molecules

B: Peroxisome proliferator-activated receptor gamma


Theoretical massNumber of molelcules
Total (without water)63,1843
Polymers62,8992
Non-polymers2851
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area1900 Å2
ΔGint-12 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.43, 62.02, 119.49
Angle α, β, γ (deg.)90, 102.09, 90
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 207 - 474 / Label seq-ID: 6 - 273

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Peroxisome proliferator-activated receptor gamma


Mass: 31449.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P37231
#2: Chemical ChemComp-AYR / (2E,4E)-5-(2H-1,3-benzodioxol-5-yl)-1-(piperidin-1-yl)penta-2,4-dien-1-one


Mass: 285.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Tris-HCl, 0.7 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→45.68 Å / Num. obs: 27580 / % possible obs: 99.6 % / Redundancy: 3.1 % / CC1/2: 0.995 / Rpim(I) all: 0.04 / Rrim(I) all: 0.058 / Net I/σ(I): 9.2
Reflection shellResolution: 2.36→2.45 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2863 / CC1/2: 0.936 / Rpim(I) all: 0.236 / Rrim(I) all: 0.344

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
iMOSFLMdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VV3

2vv3


Resolution: 2.36→45.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 18.932 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.243
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2547 1374 4.984 %
Rwork0.2006 26196 -
all0.203 --
obs-27570 99.391 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 68.131 Å2
Baniso -1Baniso -2Baniso -3
1-2.682 Å2-0 Å20.29 Å2
2---0.376 Å2-0 Å2
3----2.226 Å2
Refinement stepCycle: LAST / Resolution: 2.36→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4054 0 21 36 4111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124151
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164128
X-RAY DIFFRACTIONr_angle_refined_deg2.21.8475588
X-RAY DIFFRACTIONr_angle_other_deg0.7211.7719529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0645503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.649516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09410797
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.52510183
X-RAY DIFFRACTIONr_chiral_restr0.1040.2648
X-RAY DIFFRACTIONr_chiral_restr_other0.2380.21
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024654
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02890
X-RAY DIFFRACTIONr_nbd_refined0.2540.2978
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.23770
X-RAY DIFFRACTIONr_nbtor_refined0.1930.22094
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22339
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.050.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1460.217
X-RAY DIFFRACTIONr_nbd_other0.2520.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2140.25
X-RAY DIFFRACTIONr_mcbond_it4.3363.8772027
X-RAY DIFFRACTIONr_mcbond_other4.3353.8782027
X-RAY DIFFRACTIONr_mcangle_it5.9856.9462522
X-RAY DIFFRACTIONr_mcangle_other5.9856.9472523
X-RAY DIFFRACTIONr_scbond_it5.6584.4692124
X-RAY DIFFRACTIONr_scbond_other5.6574.472125
X-RAY DIFFRACTIONr_scangle_it8.3187.9633065
X-RAY DIFFRACTIONr_scangle_other8.3177.9663066
X-RAY DIFFRACTIONr_lrange_it10.08938.4734705
X-RAY DIFFRACTIONr_lrange_other10.08938.4774706
X-RAY DIFFRACTIONr_ncsr_local_group_10.160.057454
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.15980.05006
12AX-RAY DIFFRACTIONLocal ncs0.15980.05006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.4210.284990.2551901X-RAY DIFFRACTION99.1572
2.421-2.4870.3421080.2381871X-RAY DIFFRACTION99.6475
2.487-2.5590.299750.2421847X-RAY DIFFRACTION99.3282
2.559-2.6380.318950.2421732X-RAY DIFFRACTION99.564
2.638-2.7240.3161060.2111716X-RAY DIFFRACTION99.5628
2.724-2.8190.26920.1881689X-RAY DIFFRACTION99.4972
2.819-2.9250.303810.2171601X-RAY DIFFRACTION99.5855
2.925-3.0440.268800.2251521X-RAY DIFFRACTION99.441
3.044-3.1790.282800.2311474X-RAY DIFFRACTION99.2971
3.179-3.3330.285810.2091426X-RAY DIFFRACTION99.4063
3.333-3.5120.221660.2071372X-RAY DIFFRACTION99.5156
3.512-3.7240.319610.2541263X-RAY DIFFRACTION97.7122
3.724-3.9790.249690.2111200X-RAY DIFFRACTION99.6858
3.979-4.2950.19600.1781112X-RAY DIFFRACTION99.5752
4.295-4.7010.218450.171074X-RAY DIFFRACTION99.9107
4.701-5.2490.242470.175938X-RAY DIFFRACTION100
5.249-6.0480.313380.221842X-RAY DIFFRACTION99.435
6.048-7.3750.236450.182714X-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)
12.53520.3468-0.46562.4228-0.57313.6708-0.224-0.00720.0058-0.0020.1879-0.4101-0.35830.34480.03620.1750.06020.02530.1494-0.01540.077513.312611.87517.1585
23.47620.29630.6111.8090.42183.38290.0598-0.27230.1940.2761-0.031-0.0309-0.07070.3206-0.02890.22990.10810.08810.15690.0430.057230.5719-10.785834.1526
Refinement TLS groupSelection: ALL

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