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- PDB-9v8h: PPARgamma ligand-binding domain in complex with PG08-NL and rosig... -

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Basic information

Entry
Database: PDB / ID: 9v8h
TitlePPARgamma ligand-binding domain in complex with PG08-NL and rosiglitazone
Components
  • PG08-NL
  • 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 / beige fat cell differentiation / 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 / beige fat cell differentiation / 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 / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of cardiac muscle hypertrophy in response to stress / positive regulation of fatty acid metabolic process / STAT family protein binding / positive regulation of lipid metabolic process / WW domain binding / response to lipid / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / LBD domain binding / positive regulation of lipoprotein transport / negative regulation of SMAD protein signal transduction / lipid homeostasis / E-box binding / alpha-actinin binding / R-SMAD binding / negative regulation of blood vessel endothelial cell migration / white fat cell differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of lipid storage / positive regulation of cholesterol efflux / negative regulation of BMP signaling pathway / monocyte differentiation / cell fate commitment / BMP signaling pathway / cellular response to low-density lipoprotein particle stimulus / negative regulation of mitochondrial fission / negative regulation of osteoblast differentiation / long-chain fatty acid transport / positive regulation of fat cell differentiation / nuclear retinoid X receptor binding / fat cell differentiation / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / intracellular receptor signaling pathway / negative regulation of MAPK cascade / peptide binding / cell maturation / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / regulation of cellular response to insulin stimulus / positive regulation of adipose tissue development / response to nutrient / negative regulation of miRNA transcription / placenta development / brown fat cell differentiation / negative regulation of angiogenesis / Regulation of PTEN gene transcription / transcription coregulator binding / positive regulation of apoptotic signaling pathway / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / PPARA activates gene expression / fatty acid metabolic process / regulation of circadian rhythm / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / positive regulation of miRNA transcription / mRNA transcription by RNA polymerase II / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / regulation of blood pressure / nuclear receptor activity / RNA polymerase II transcription regulator complex / 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 / signaling 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 / 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 / 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-BRL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 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: J.Am.Chem.Soc. / Year: 2025
Title: De Novo Discovery of alpha , alpha-Disubstituted alpha-amino Acid-Containing alpha-helical Peptides as Competitive PPAR gamma PPI Inhibitors.
Authors: Sigal, M. / Egner, M. / Okada, C. / Merk, D. / Sengoku, T. / Katoh, T. / Suga, H.
History
DepositionMay 29, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 19, 2025Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 3, 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: PG08-NL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1975
Polymers33,5832
Non-polymers6143
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-12 kcal/mol
Surface area13110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.690, 53.470, 66.830
Angle α, β, γ (deg.)90.00, 106.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 31449.520 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 PG08-NL


Mass: 2133.579 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 246 molecules

#3: Chemical ChemComp-BRL / 2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) / BRL49653 / ROSIGLITAZONE


Mass: 357.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19N3O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium malonate (pH 7.5 to 8.0) and 15 to 20% PEG 3,350

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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: 1.39→41.89 Å / Num. obs: 59561 / % possible obs: 100 % / Redundancy: 70.7 % / CC1/2: 1 / Net I/σ(I): 20
Reflection shellResolution: 1.39→1.44 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5973 / CC1/2: 0.681

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Processing

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

8hum


Resolution: 1.39→32.06 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.986 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1982 3.3 %RANDOM
Rwork0.16292 ---
obs0.16378 57550 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.893 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20.2 Å2
2---0.3 Å20 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 1.39→32.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 42 243 2401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122230
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162216
X-RAY DIFFRACTIONr_angle_refined_deg2.0571.8353011
X-RAY DIFFRACTIONr_angle_other_deg0.6731.755117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2295270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.831514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50110412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1110.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022495
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02472
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_it1.9570.9231080
X-RAY DIFFRACTIONr_mcbond_other1.9520.9211079
X-RAY DIFFRACTIONr_mcangle_it3.0471.6131350
X-RAY DIFFRACTIONr_mcangle_other3.0481.6131351
X-RAY DIFFRACTIONr_scbond_it3.3811.3981150
X-RAY DIFFRACTIONr_scbond_other3.3791.3991151
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2392.351662
X-RAY DIFFRACTIONr_long_range_B_refined8.19813.292649
X-RAY DIFFRACTIONr_long_range_B_other8.08411.442564
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.39→1.426 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 147 -
Rwork0.432 4271 -
obs--99.91 %
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)
10.47840.329-0.30620.4519-0.50970.62660.03940.07210.030.05860.02480.0972-0.0349-0.0295-0.06420.1705-0.0090.0150.1364-0.00150.1478-23.3415-5.7010.3038
20.64760.3513-1.29111.9251-0.32.6822-0.18110.1608-0.0403-0.15490.0784-0.10860.343-0.33920.10270.2308-0.0642-0.01190.1577-0.03760.1038-17.7907-15.4659-15.4652
30.3970.56810.47511.29581.9033.6743-0.14010.3450.0117-0.06780.2574-0.02460.1281-0.153-0.11730.2951-0.12060.00720.43110.01170.0386-10.2275-17.8839-31.9441
41.0647-0.5044-1.18470.69810.65351.51480.05830.02770.0441-0.2007-0.00470.0367-0.0679-0.047-0.05360.22820.00950.01120.12880.00190.1039-10.7162-1.1707-21.639
50.1394-0.1235-0.13510.63910.20860.49390.00240.00940.047-0.06360.00820.00010.01010.0148-0.01060.17510.00320.00490.1206-0.00630.1379-11.05493.2998-8.5949
60.6875-0.0201-0.22110.20070.04211.6591-0.06630.0301-0.0421-0.0887-0.0172-0.08270.18540.11030.08350.22220.02430.02740.1106-0.01830.1149-3.1127-14.518-20.4867
70.36290.3965-0.12850.9727-0.2570.12960.0169-0.03530.00020.0223-0.008-0.01680.0170.0375-0.00880.1689-0.0051-0.00330.1243-0.0010.1411-11.7649-3.99741.8513
80.96630.7556-0.27510.7476-0.7241.8247-0.09860.0435-0.0452-0.02430.0039-0.0735-0.04480.12550.09470.15660.01310.00590.15040.01940.15711.5549-4.6676-10.479
92.48340.909-0.4610.3913-0.01151.65480.12650.03210.1093-0.06340.0489-0.0528-0.08410.0588-0.17530.3099-0.030.14530.115-0.01430.2132-2.02236.6733-21.4791
103.06620.57641.42.71061.52645.9220.20680.28120.2176-0.044-0.0354-0.0906-0.42220.2201-0.17150.2368-0.02840.06980.08710.02860.14-8.048416.7422-14.1167
113.7657-1.5714-1.43752.25351.1261.92880.2255-0.0046-0.0621-0.1427-0.0502-0.0241-0.049-0.0513-0.17530.18010.00810.01920.13030.00240.1216-14.980811.0102-14.5564
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A207 - 225
2X-RAY DIFFRACTION2A226 - 238
3X-RAY DIFFRACTION3A239 - 276
4X-RAY DIFFRACTION4A277 - 302
5X-RAY DIFFRACTION5A303 - 333
6X-RAY DIFFRACTION6A334 - 377
7X-RAY DIFFRACTION7A378 - 430
8X-RAY DIFFRACTION8A431 - 459
9X-RAY DIFFRACTION9A460 - 477
10X-RAY DIFFRACTION10B6 - 13
11X-RAY DIFFRACTION11B14 - 18

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