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- PDB-9gvt: Human PPAR-gamma ligand binding domain in complex with AK176_D -

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Basic information

Entry
Database: PDB / ID: 9gvt
TitleHuman PPAR-gamma ligand binding domain in complex with AK176_D
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 / E-box binding / lipid homeostasis / 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 / 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 / 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: 2.3 Å
AuthorsKoops, A.A. / Oerlemans, G.J.M. / Brunsveld, L.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: To Be Published
Title: Molecule name: Peroxisome proliferator-activated receptor gamma Ligand Binding Domain
Authors: Koops, A.A. / Oerlemans, G.J.M. / Brunsveld, L.
History
DepositionSep 25, 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)63,4563
Polymers62,8212
Non-polymers6351
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-4 kcal/mol
Surface area24110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.730, 61.200, 118.362
Angle α, β, γ (deg.)90.000, 102.217, 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 233 through 251 or (resid 252...
d_2ens_1(chain "B" and (resid 233 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_11HISHISAB233 - 2683 - 38
d_12LYSLYSAB272 - 50242 - 272
d_21HISHISBA233 - 2913 - 61
d_22LYSLYSBA303 - 50273 - 272

NCS oper: (Code: givenMatrix: (0.10311083265728, 0.97895545655347, 0.17610897272116), (0.98372828547391, -0.12655460088372, 0.12752487347075), (0.14712857148525, 0.16009418190348, -0.9760753231044) ...NCS oper: (Code: given
Matrix: (0.10311083265728, 0.97895545655347, 0.17610897272116), (0.98372828547391, -0.12655460088372, 0.12752487347075), (0.14712857148525, 0.16009418190348, -0.9760753231044)
Vector: 14.880280100956, -23.800006130367, 46.851895820354)

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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
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37231
#2: Chemical ChemComp-A1IPQ / 4-[1-[2-chloranyl-6-(trifluoromethyl)phenyl]carbonyl-5-(trifluoromethyloxy)indazol-3-yl]-3-phenylmethoxy-benzoic acid


Mass: 634.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H17ClF6N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
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: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 9, 2024
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.3→33.02 Å / Num. obs: 29022 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 47.45 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.1
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2810 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5phasing
PHENIX1.21.2-5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→33.02 Å / SU ML: 0.3755 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.5418
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2519 1483 5.11 %
Rwork0.2126 27520 -
obs0.2146 29003 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→33.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4049 0 44 20 4113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00894165
X-RAY DIFFRACTIONf_angle_d1.07315641
X-RAY DIFFRACTIONf_chiral_restr0.0542662
X-RAY DIFFRACTIONf_plane_restr0.0075717
X-RAY DIFFRACTIONf_dihedral_angle_d19.36631524
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.3486411244936 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.39031240.35032480X-RAY DIFFRACTION99.96
2.37-2.460.33941490.31172453X-RAY DIFFRACTION100
2.46-2.560.31631380.28062484X-RAY DIFFRACTION99.96
2.56-2.670.28421320.26552499X-RAY DIFFRACTION99.89
2.67-2.810.37191410.26422463X-RAY DIFFRACTION99.92
2.81-2.990.32721450.25692471X-RAY DIFFRACTION99.89
2.99-3.220.28661240.24782537X-RAY DIFFRACTION100
3.22-3.550.30081250.2222507X-RAY DIFFRACTION100
3.55-4.060.20571240.18222530X-RAY DIFFRACTION99.92
4.06-5.110.20411400.16312525X-RAY DIFFRACTION100
5.11-33.020.20631410.18382571X-RAY DIFFRACTION99.6
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)
11.93362542707020.047708060529339-0.33012819403481.2651555035875-0.0547889682176982.47213797984860.074034648257911-0.23938964882785-0.0244853120276420.1590506908370.00326939075556470.032416046563404-0.0457100381986650.254872498562820.000294419904413810.292193936706780.0708176704869240.0152784381607350.216028786948250.0339848099832220.2969879170398930.637983101263-10.28168576725634.105914126746
21.90253441590080.12087505907681-0.328760235410091.31823355461720.0774441130770492.6449570932511-0.11883902706631-0.0127456372928210.014754894646154-0.0349963249468330.17505094129061-0.12986046799467-0.191755353312860.228713064879840.000343285191721960.317338394532670.066024425219555-0.0179981958312560.398471412361330.0325365921719930.3520257156907612.78372601846911.29188938669816.835176233754
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 233:601)BA - B233 - 6011
22(chain A and resseq 233:503)AC233 - 5031 - 260

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