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- PDB-9gwh: Human PPAR-gamma ligand binding domain in complex with LW77 -

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Basic information

Entry
Database: PDB / ID: 9gwh
TitleHuman PPAR-gamma ligand binding domain in complex with LW77
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 / 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
: / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOerlemans, G.J.M. / Koops, A.A. / Brunsveld, L.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: 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.
History
DepositionSep 26, 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

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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)63,9924
Polymers62,8212
Non-polymers1,1712
Water68538
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: PPARg is known to form homodimers in this space group
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-5 kcal/mol
Surface area24010 Å2
Unit cell
Length a, b, c (Å)94.268, 62.109, 119.798
Angle α, β, γ (deg.)90.000, 101.900, 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 235 through 251 or (resid 252...
d_2ens_1(chain "B" and (resid 235 through 243 or (resid 244...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLUTHRTHRAA235 - 2692 - 36
d_12ASPASPASPASPAA271 - 50338 - 259
d_13L77L77L77L77AC601
d_21GLUGLUPHEPHEBB235 - 2921 - 57
d_22GLUGLUASPASPBB304 - 50364 - 263
d_23L77L77L77L77BD601

NCS oper: (Code: givenMatrix: (0.0865654860114, 0.981180154969, 0.172603360704), (0.984809214588, -0.110454594628, 0.133979824557), (0.150523179259, 0.158383351461, -0.975836813451)Vector: 15. ...NCS oper: (Code: given
Matrix: (0.0865654860114, 0.981180154969, 0.172603360704), (0.984809214588, -0.110454594628, 0.133979824557), (0.150523179259, 0.158383351461, -0.975836813451)
Vector: 15.3901053647, -24.5348755683, 47.1758618891)

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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-A1IP0 / 4-[5-chloranyl-1-[2-chloranyl-6-(trifluoromethyl)phenyl]carbonyl-indazol-3-yl]-2-phenylmethoxy-benzoic acid


Mass: 585.357 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H17Cl2F3N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.8 Å3/Da / Density % sol: 56.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.9M-1.2M sodium citrate tribasic dihydrate, 0.1M sodium cacodylate pH 6.4-7.4
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: 0.873128 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 2.1→46.29 Å / Num. obs: 39519 / % possible obs: 99.5 % / Redundancy: 6.9 % / CC1/2: 0.999 / Net I/σ(I): 11.1
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 3221 / CC1/2: 0.784

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB-REDOrefinement
REFMACV5refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.29 Å / SU ML: 0.3462 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.6267
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 1862 4.72 %RANDOM
Rwork0.2172 37619 --
obs0.219 39481 99.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.83 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3975 0 80 38 4093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00854129
X-RAY DIFFRACTIONf_angle_d0.97475609
X-RAY DIFFRACTIONf_chiral_restr0.0492661
X-RAY DIFFRACTIONf_plane_restr0.0118713
X-RAY DIFFRACTIONf_dihedral_angle_d8.8024573
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.252108428 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.38311450.36172850X-RAY DIFFRACTION99.21
2.16-2.220.40861390.3452876X-RAY DIFFRACTION99.5
2.22-2.290.40391350.36072856X-RAY DIFFRACTION98.68
2.29-2.370.3531570.27942879X-RAY DIFFRACTION99.12
2.37-2.470.32781280.2572886X-RAY DIFFRACTION99.18
2.47-2.580.26361630.25832855X-RAY DIFFRACTION99.34
2.58-2.720.31751360.25982892X-RAY DIFFRACTION99.44
2.72-2.890.32461400.24712887X-RAY DIFFRACTION99.51
2.89-3.110.26891440.252904X-RAY DIFFRACTION99.22
3.11-3.420.31251510.2412881X-RAY DIFFRACTION99.28
3.42-3.920.25341670.20442901X-RAY DIFFRACTION99.64
3.92-4.930.19241250.16552943X-RAY DIFFRACTION99.58
4.94-46.290.18361320.17433009X-RAY DIFFRACTION98.93
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)
12.348626500140.345784089785-0.5186662634771.476660621430.6187147751263.33069630472-0.298783736915-0.0821536439379-0.05495025791960.07520453254950.233421577786-0.182350135563-0.2907976542460.474439520952-0.002823637028590.2943568647110.0919964452223-0.05110607595140.4041169888020.05242823021750.37740690810512.827938372911.662822235917.118277754
21.977206061640.181213949327-0.06210611077921.336503403650.3118191624943.035831135710.0331883745201-0.104925214905-0.05938191612740.295113055980.04604289631620.0650332394082-0.2974665229760.3106767756920.00375059181010.4172008971350.1467040381140.03094067077620.2462506799470.02516003096290.33093796707331.570069517-10.527204816634.68248716
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resseq 234:503)AA234 - 5031 - 259
22(chain B and resseq 235:503)BB235 - 5031 - 263

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