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- PDB-9v8f: PPARgamma ligand-binding domain in complex with PG14 -

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Basic information

Entry
Database: PDB / ID: 9v8f
TitlePPARgamma ligand-binding domain in complex with PG14
Components
  • PG14
  • Peroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / Nuclear receptor / de novo peptide
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
DI(HYDROXYETHYL)ETHER / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSigal, M. / Okada, C. / Katoh, T. / Suga, H. / Sengoku, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: To Be Published
Title: PPARgamma ligand-binding domain in complex with PG14
Authors: Sigal, M.
History
DepositionMay 29, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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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: PG14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5924
Polymers33,3802
Non-polymers2122
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-8 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.510, 85.140, 99.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 31208.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli (E. coli) / References: UniProt: P37231
#2: Protein/peptide PG14


Mass: 2171.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris HCl (pH 6.2 to 6.5), 23% PEG 3,350, and 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→43.01 Å / Num. obs: 28845 / % possible obs: 100 % / Redundancy: 84.6 % / CC1/2: 0.999 / Net I/σ(I): 23.6
Reflection shellResolution: 1.75→1.86 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4714 / CC1/2: 0.926

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XSCALEdata scaling
PARROTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8HUM

8hum


Resolution: 1.75→43.05 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.049 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23042 1629 5.7 %RANDOM
Rwork0.19158 ---
obs0.19375 27134 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.387 Å2
Baniso -1Baniso -2Baniso -3
1-4.23 Å20 Å2-0 Å2
2---2.32 Å20 Å2
3----1.92 Å2
Refinement stepCycle: 1 / Resolution: 1.75→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 14 145 2379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122271
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162242
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.8463059
X-RAY DIFFRACTIONr_angle_other_deg0.6171.7615170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.11859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51210427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0960.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022523
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02477
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9442.0171103
X-RAY DIFFRACTIONr_mcbond_other1.9432.0181104
X-RAY DIFFRACTIONr_mcangle_it33.5991372
X-RAY DIFFRACTIONr_mcangle_other2.9993.5991373
X-RAY DIFFRACTIONr_scbond_it2.7572.4311168
X-RAY DIFFRACTIONr_scbond_other2.7582.4321169
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4354.2841688
X-RAY DIFFRACTIONr_long_range_B_refined6.9721.82687
X-RAY DIFFRACTIONr_long_range_B_other6.9421.382652
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 118 -
Rwork0.341 1968 -
obs--99.9 %
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)
11.55222.75253.52225.69345.93618.23410.07910.1906-0.0856-0.52110.0052-0.49780.34110.728-0.08430.63710.24240.14780.38620.08510.268719.9421-2.387211.174
20.7952-0.5535-0.59651.1009-0.64993.98830.0551-0.10570.06230.08250.05980.0619-0.25060.2401-0.11490.045-0.04470.0030.1181-0.02860.109819.34268.836338.0044
30.3043-0.41810.25911.745-1.86393.07930.1154-0.0493-0.0151-0.04640.0960.3141-0.0542-0.0623-0.21140.0626-0.0090.00050.11840.02530.155511.43379.648930.6778
41.024-0.66640.24521.4373-0.82561.95220.23260.0816-0.1994-0.5149-0.03090.44010.4058-0.1454-0.20160.2041-0.0169-0.17050.10680.00080.22068.10640.648718.1978
51.0748-0.23530.045812.1685.25344.5518-0.2250.0280.20840.20940.31851.23480.2008-0.1921-0.09350.0578-0.0156-0.07250.11240.09230.40391.5468.903728.5887
60.1558-0.8074-0.48414.86222.21434.61-0.06-0.06220.05290.43090.20190.184-0.2118-0.0698-0.14190.18220.05480.04450.1921-0.06240.37918.247923.40130.4537
76.1801-1.77661.95443.3337-2.73185.70530.04410.01060.14730.13890.09890.254-0.1692-0.176-0.14310.12920.02840.02620.02680.05350.154211.386427.841715.0878
80.7293-0.53581.14383.2381-1.574910.19230.00130.0720.13620.07210.076-0.2062-0.32390.2087-0.07740.10280.0199-0.00380.08070.02170.158617.951222.738519.3638
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A205 - 225
2X-RAY DIFFRACTION2A226 - 302
3X-RAY DIFFRACTION3A303 - 364
4X-RAY DIFFRACTION4A365 - 430
5X-RAY DIFFRACTION5A431 - 459
6X-RAY DIFFRACTION6A460 - 477
7X-RAY DIFFRACTION7B2 - 10
8X-RAY DIFFRACTION8B11 - 17

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