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- PDB-7efq: Crystal structure of hPPARgamma ligand binding domain complexed w... -

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Basic information

Entry
Database: PDB / ID: 7efq
TitleCrystal structure of hPPARgamma ligand binding domain complexed with rosiglitazone-based fluorescence probe
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / PPARgamma / rosiglitazone / coumarin / fluorescence probe / TZD
Function / homology
Function and homology information


prostaglandin receptor activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / positive regulation of cholesterol transport / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of low-density lipoprotein receptor activity ...prostaglandin receptor activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / positive regulation of cholesterol transport / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of low-density lipoprotein receptor activity / arachidonate binding / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / DNA binding domain binding / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / WW domain binding / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / LBD domain binding / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / E-box binding / alpha-actinin binding / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / white fat cell differentiation / negative regulation of BMP signaling pathway / cell fate commitment / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / negative regulation of MAPK cascade / BMP signaling pathway / retinoic acid receptor signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cell maturation / epithelial cell differentiation / negative regulation of signaling receptor activity / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / regulation of cellular response to insulin stimulus / negative regulation of angiogenesis / response to nutrient / negative regulation of miRNA transcription / Regulation of PTEN gene transcription / transcription coregulator binding / fatty acid metabolic process / negative regulation of smooth muscle cell proliferation / positive regulation of apoptotic signaling pathway / negative regulation of transforming growth factor beta receptor signaling pathway / peptide binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / regulation of circadian rhythm / placenta development / PPARA activates gene expression / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / positive regulation of miRNA transcription / regulation of blood pressure / cellular response to insulin stimulus / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / rhythmic process / glucose homeostasis / cellular response to hypoxia / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / intracellular membrane-bounded organelle / 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 / Zinc finger, C4 type (two domains) / 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 / Zinc finger, C4 type (two domains) / 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-J3F / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYoshikawa, C. / Ishida, H. / Ohashi, N. / Itoh, T.
CitationJournal: Int J Mol Sci / Year: 2021
Title: Synthesis of a Coumarin-Based PPAR gamma Fluorescence Probe for Competitive Binding Assay.
Authors: Yoshikawa, C. / Ishida, H. / Ohashi, N. / Itoh, T.
History
DepositionMar 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3953
Polymers62,8992
Non-polymers4961
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.330, 61.900, 119.370
Angle α, β, γ (deg.)90.000, 102.290, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-505-

HOH

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Components

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


Mass: 31449.520 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: Chemical ChemComp-J3F / (5S)-5-[[4-[2-[[7-(diethylamino)-2-oxidanylidene-chromen-4-yl]-methyl-amino]ethoxy]phenyl]methyl]-1,3-thiazolidine-2,4-dione


Mass: 495.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H29N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: One microliter of PPARgamma-LBD solution (6 mg/mL, in 20 mM Tris-HCl pH 8.0, 1 mM TCEP, 0.5 mM EDTA) with 0.5 equiv. ligand with 1 microliter of reservoir solution (0.8 M sodium citrate and ...Details: One microliter of PPARgamma-LBD solution (6 mg/mL, in 20 mM Tris-HCl pH 8.0, 1 mM TCEP, 0.5 mM EDTA) with 0.5 equiv. ligand with 1 microliter of reservoir solution (0.8 M sodium citrate and 0.1 M Tris-HCl pH 7.3). Drops were equilibrated against 300 microliter of reservoir solution at 293K.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→26.75 Å / Num. obs: 29512 / % possible obs: 99.1 % / Redundancy: 3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.042 / Rrim(I) all: 0.06 / Net I/σ(I): 14.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.91-26.753.40.0175330.9990.0170.024
2.3-2.382.90.34828290.8580.3310.481

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
pointless1.9.23data reduction
PHASER2.8.3phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vv3

2vv3


Resolution: 2.3→26.75 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.916 / SU B: 18.497 / SU ML: 0.207 / Cross valid method: FREE R-VALUE / ESU R: 0.32 / ESU R Free: 0.24
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2644 1515 5.135 %
Rwork0.2243 27987 -
all0.226 --
obs-29502 98.904 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 49.828 Å2
Baniso -1Baniso -2Baniso -3
1--0.595 Å2-0 Å20.453 Å2
2--0.218 Å2-0 Å2
3---0.165 Å2
Refinement stepCycle: LAST / Resolution: 2.3→26.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4058 0 35 72 4165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0134161
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174121
X-RAY DIFFRACTIONr_angle_refined_deg1.8861.6355609
X-RAY DIFFRACTIONr_angle_other_deg1.3781.589503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23224.205195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.35515786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5411515
X-RAY DIFFRACTIONr_chiral_restr0.0880.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024572
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02879
X-RAY DIFFRACTIONr_nbd_refined0.2350.2949
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.23680
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22042
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21927
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.294
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2290.220
X-RAY DIFFRACTIONr_nbd_other0.2230.281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.27
X-RAY DIFFRACTIONr_mcbond_it1.7743.1042037
X-RAY DIFFRACTIONr_mcbond_other1.7483.1022036
X-RAY DIFFRACTIONr_mcangle_it2.6574.6432534
X-RAY DIFFRACTIONr_mcangle_other2.6584.6452535
X-RAY DIFFRACTIONr_scbond_it2.2113.3672124
X-RAY DIFFRACTIONr_scbond_other2.213.3682125
X-RAY DIFFRACTIONr_scangle_it3.4274.9433075
X-RAY DIFFRACTIONr_scangle_other3.4274.9443076
X-RAY DIFFRACTIONr_lrange_it4.79437.064620
X-RAY DIFFRACTIONr_lrange_other4.79237.0524618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.3111010.2952011X-RAY DIFFRACTION96.3943
2.36-2.4240.3051180.2761993X-RAY DIFFRACTION98.0492
2.424-2.4950.2811090.2551920X-RAY DIFFRACTION98.3043
2.495-2.5710.3161050.2651858X-RAY DIFFRACTION98.0519
2.571-2.6560.322970.2631845X-RAY DIFFRACTION97.6861
2.656-2.7490.2791080.2491729X-RAY DIFFRACTION98.4987
2.749-2.8530.299850.2441736X-RAY DIFFRACTION99.8355
2.853-2.9690.3091060.2581677X-RAY DIFFRACTION99.7204
2.969-3.1010.284750.2521597X-RAY DIFFRACTION99.9402
3.101-3.2520.271810.2491530X-RAY DIFFRACTION100
3.252-3.4280.277720.2371464X-RAY DIFFRACTION99.9349
3.428-3.6360.288690.2341386X-RAY DIFFRACTION99.5212
3.636-3.8860.253520.2121309X-RAY DIFFRACTION99.707
3.886-4.1970.208700.1821213X-RAY DIFFRACTION99.9221
4.197-4.5970.222700.171109X-RAY DIFFRACTION99.7462
4.597-5.1390.267550.1891017X-RAY DIFFRACTION99.2593
5.139-5.9320.298500.256896X-RAY DIFFRACTION100
5.932-7.2610.296380.224762X-RAY DIFFRACTION100
7.261-10.2480.189330.16615X-RAY DIFFRACTION100
10.248-26.7521320X-RAY DIFFRACTION93.1694
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)
12.58350.7763-0.45861.8621-0.11153.1827-0.09960.0095-0.0268-0.08450.1165-0.235-0.21080.3207-0.01690.07590.02910.01680.1013-0.01060.032913.169110.94616.8616
22.53590.00650.44461.55410.44543.60880.0731-0.30340.17960.25270.0115-0.0531-0.22860.3009-0.08460.16580.04150.05760.14170.01220.046230.4024-11.996433.9098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA207 - 474
2X-RAY DIFFRACTION2ALLB207 - 474

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