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- PDB-9gwk: Human PPAR-gamma ligand binding domain in complex with AKGO6A -

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Basic information

Entry
Database: PDB / ID: 9gwk
TitleHuman PPAR-gamma ligand binding domain in complex with AKGO6A
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / PPAR / PPAR gamma / PPARg / peroxisome proliferator-activated receptor gamma / nuclear receptor / transcription factor / partial agonist / agonist
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 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 / 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 / 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 / positive regulation of apoptotic signaling pathway / Regulation of PTEN gene transcription / transcription coregulator binding / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / mRNA transcription by RNA polymerase II / fatty acid metabolic process / negative regulation of transforming growth factor beta receptor signaling pathway / 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 / 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
: / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKoops, A.A. / Oerlemans, G.J.M. / Brunsveld, L.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
Citation
Journal: To Be Published
Title: Development and characterization of novel indazole-based PPAR-gamma partial agonists
Authors: Koops, A.A. / Oerlemans, G.J.M. / Brunsveld, L.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionSep 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Peroxisome proliferator-activated receptor gamma
A: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4063
Polymers62,8212
Non-polymers5851
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, NR's are known to form homodimers in crystallization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-3 kcal/mol
Surface area24590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.607, 62.020, 119.462
Angle α, β, γ (deg.)90.000, 101.830, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 234 through 251 or (resid 252...
d_2ens_1(chain "B" and (resid 234 through 243 or (resid 244...

NCS domain segments:

Ens-ID: ens_1 / End auth comp-ID: LYS / End label comp-ID: LYS

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETAB234 - 2684 - 38
d_12LYSLYSAB272 - 29142 - 61
d_13LYSLYSAB303 - 50273 - 272
d_21METMETBA234 - 2914 - 61
d_22LYSLYSBA29363
d_23GLUGLUBA304 - 50274 - 272

NCS oper: (Code: givenMatrix: (0.10091118018965, 0.98042310475158, 0.16907829364528), (0.98363874261529, -0.12381049146814, 0.13086552727374), (0.14923725318749, 0.15310616536144, -0.97687601280273) ...NCS oper: (Code: given
Matrix: (0.10091118018965, 0.98042310475158, 0.16907829364528), (0.98363874261529, -0.12381049146814, 0.13086552727374), (0.14923725318749, 0.15310616536144, -0.97687601280273)
Vector: 15.121135289446, -24.372106346868, 47.229090704549)

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Components

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


Mass: 31410.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal GSHM left from Thrombin cleavage / Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37231
#2: Chemical ChemComp-A1IP9 / 4-[7-chloranyl-1-[2-chloranyl-6-(trifluoromethyl)phenyl]carbonyl-indazol-3-yl]-3-phenylmethoxy-benzoic acid


Mass: 585.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H17Cl2F3N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.9M-1.2M sodium citrate tribasic dihydrate, 0.1M sodium cacodylate
PH range: 6.4-7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 16, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.2→45.97 Å / Num. obs: 34130 / % possible obs: 99.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 52.37 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.6
Reflection shellResolution: 2.2→2.27 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2964 / CC1/2: 0.885

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Processing

Software
NameVersionClassification
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5refinement
PDB-REDOrefinement
Cootmodel building
PHENIX1.21.2-5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.97 Å / SU ML: 0.3004 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.0772
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2543 1704 5 %
Rwork0.2148 32406 -
obs0.2166 34110 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.45 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4045 0 40 23 4108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094157
X-RAY DIFFRACTIONf_angle_d1.04995632
X-RAY DIFFRACTIONf_chiral_restr0.0556662
X-RAY DIFFRACTIONf_plane_restr0.0111718
X-RAY DIFFRACTIONf_dihedral_angle_d16.83521520
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.4860842665345 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.29991300.30752727X-RAY DIFFRACTION99.83
2.26-2.340.30231570.28342644X-RAY DIFFRACTION99.36
2.34-2.420.30191220.26372687X-RAY DIFFRACTION99.36
2.42-2.520.33011480.25732659X-RAY DIFFRACTION99.54
2.52-2.630.30031480.26622667X-RAY DIFFRACTION99.43
2.63-2.770.28091310.24342728X-RAY DIFFRACTION99.48
2.77-2.950.29191450.24962702X-RAY DIFFRACTION99.44
2.95-3.170.31121460.27612657X-RAY DIFFRACTION99.47
3.17-3.490.2691480.23552701X-RAY DIFFRACTION99.65
3.49-40.22641700.20542708X-RAY DIFFRACTION99.79
4-5.030.22071350.17422729X-RAY DIFFRACTION99.76
5.04-45.970.22961240.18442797X-RAY DIFFRACTION99.02
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)
12.34778027342960.20699597621959-0.353612585795281.63340179111640.204845084045852.71384517000980.091094447378652-0.21246452853376-0.0533354753641620.205737897675490.029791301904780.0099365868624379-0.135731187487740.268947060537730.00184107496856930.332238477576550.14018507321720.00828158839035460.218891349980070.050388695846780.3166432466367231.300238450215-10.49332225613634.548092182134
22.33419882963930.193765232290340.0052382408285531.63244386774280.514338272360033.2578537733861-0.22382289007144-0.041364519669454-0.0094619286813324-0.0733111915860210.26333310845612-0.20762389646477-0.263401014245190.321672127768040.000605768141810440.354800012564880.1086940306335-0.0144343600622870.420213615496870.0286546645795090.3960930871615813.0080297795311.55061644101817.038205359429
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain B and resseq 234:601)BA - C234 - 6011
22(chain A and resseq 233:503)AB233 - 5031 - 261

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