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- PDB-6k0t: Crystal Structure of PPARgamma Ligand Binding Domain in complex w... -

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Basic information

Entry
Database: PDB / ID: 6k0t
TitleCrystal Structure of PPARgamma Ligand Binding Domain in complex with dibenzooxepine derivative compound-17
Components
  • Peroxisome proliferator-activated receptor gamma
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
KeywordsNUCLEAR PROTEIN / PPARgamma / Ligand binding domain / PPARg modulator / Cancer
Function / homology
Function and homology information


Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / cellular respiration / 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 / Activation of PPARGC1A (PGC-1alpha) by phosphorylation ...Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / cellular respiration / 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 / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / 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 / STAT family protein binding / positive regulation of fatty acid metabolic process / temperature homeostasis / response to lipid / response to muscle activity / negative regulation of SMAD protein signal transduction / lncRNA binding / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / response to starvation / lipid homeostasis / E-box binding / intracellular glucose homeostasis / alpha-actinin binding / negative regulation of vascular associated smooth muscle cell proliferation / fatty acid oxidation / R-SMAD binding / response to dietary excess / 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 / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / cell fate commitment / negative regulation of osteoblast differentiation / positive regulation of fat cell differentiation / negative regulation of MAPK cascade / adipose tissue development / BMP signaling pathway / long-chain fatty acid transport / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / nuclear retinoid X receptor binding / brown fat cell differentiation / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cell maturation / energy homeostasis / intracellular receptor signaling pathway / digestion / positive regulation of adipose tissue development / hormone-mediated signaling pathway / peroxisome proliferator activated receptor signaling pathway / epithelial cell differentiation / regulation of cellular response to insulin stimulus / response to nutrient / positive regulation of gluconeogenesis / peptide binding / negative regulation of miRNA transcription / RNA splicing / SUMOylation of transcription cofactors / negative regulation of angiogenesis / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / positive regulation of apoptotic signaling pathway / Regulation of PTEN gene transcription / nuclear receptor binding / gluconeogenesis / fatty acid metabolic process / respiratory electron transport chain / mitochondrion organization / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / placenta development / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / regulation of circadian rhythm / PML body / Nuclear Receptor transcription pathway / chromatin DNA binding
Similarity search - Function
PGC-1alpha, RNA recognition motif / PGC-1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X Receptor / RNA recognition motif ...PGC-1alpha, RNA recognition motif / PGC-1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X Receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / 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 / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-CTU / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsSuzuki, M. / Yamamoto, K. / Takahashi, Y. / Saito, J.
CitationJournal: Bioorg.Med.Chem. / Year: 2019
Title: Development of a novel class of peroxisome proliferator-activated receptor (PPAR) gamma ligands as an anticancer agent with a unique binding mode based on a non-thiazolidinedione scaffold.
Authors: Yamamoto, K. / Tamura, T. / Nakamura, R. / Hosoe, S. / Matsubara, M. / Nagata, K. / Kodaira, H. / Uemori, T. / Takahashi, Y. / Suzuki, M. / Saito, J.I. / Ueno, K. / Shuto, S.
History
DepositionMay 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
C: Peroxisome proliferator-activated receptor gamma
D: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3096
Polymers68,2514
Non-polymers1,0582
Water8,089449
1
A: Peroxisome proliferator-activated receptor gamma
B: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6553
Polymers34,1262
Non-polymers5291
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-9 kcal/mol
Surface area13420 Å2
MethodPISA
2
C: Peroxisome proliferator-activated receptor gamma
D: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6553
Polymers34,1262
Non-polymers5291
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-9 kcal/mol
Surface area14190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.340, 54.060, 70.490
Angle α, β, γ (deg.)94.26, 103.94, 89.95
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 32769.941 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 (E. coli) / References: UniProt: P37231
#2: Protein/peptide Peroxisome proliferator-activated receptor gamma coactivator 1-alpha


Mass: 1355.662 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2*PLUS
#3: Chemical ChemComp-CTU / 3-[(1~{E})-1-[8-[(8-chloranyl-2-cyclopropyl-imidazo[1,2-a]pyridin-3-yl)methyl]-3-fluoranyl-6~{H}-benzo[c][1]benzoxepin-11-ylidene]ethyl]-4~{H}-1,2,4-oxadiazol-5-one


Mass: 528.961 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H22ClFN4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05M Magnesium acetate, 0.1M Sodium acetate, 12% PEG 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.84→43.96 Å / Num. obs: 52839 / % possible obs: 95.8 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 5.3
Reflection shellResolution: 1.84→1.94 Å / Redundancy: 2 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7640 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→40 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.2 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.146 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24425 2650 5 %RANDOM
Rwork0.19212 ---
obs0.1947 50181 95.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20.02 Å20.84 Å2
2---0.75 Å2-0.25 Å2
3---0.76 Å2
Refinement stepCycle: 1 / Resolution: 1.84→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4419 0 76 449 4944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134646
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174518
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.6696287
X-RAY DIFFRACTIONr_angle_other_deg1.3231.59110537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9785567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07424.206214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26615897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6451517
X-RAY DIFFRACTIONr_chiral_restr0.0750.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025027
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02870
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_it1.051.7942220
X-RAY DIFFRACTIONr_mcbond_other1.051.7942219
X-RAY DIFFRACTIONr_mcangle_it1.8222.6742770
X-RAY DIFFRACTIONr_mcangle_other1.8222.6742771
X-RAY DIFFRACTIONr_scbond_it1.0991.9482426
X-RAY DIFFRACTIONr_scbond_other1.0981.9482426
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8452.8733500
X-RAY DIFFRACTIONr_long_range_B_refined5.59722.5895563
X-RAY DIFFRACTIONr_long_range_B_other5.46721.9095446
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.838→1.886 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 198 -
Rwork0.349 3654 -
obs--94.92 %
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)
11.95230.08630.47283.2557-0.44881.67550.0688-0.31510.0470.6371-0.0251-0.1062-0.19880.2157-0.04360.1363-0.0374-0.01360.1074-0.0210.0081-8.65413.30612.753
21.8841-0.35160.35983.26110.53221.93160.11350.30490.0778-0.6843-0.12610.1278-0.3011-0.23680.01250.16720.0647-0.02190.09630.01420.01068.56140.193-13.593
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A205 - 477
2X-RAY DIFFRACTION1B141 - 150
3X-RAY DIFFRACTION2C205 - 477
4X-RAY DIFFRACTION2D139 - 150

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