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- PDB-6c5q: PPARg LBD bound to SR10171 -

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Basic information

Entry
Database: PDB / ID: 6c5q
TitlePPARg LBD bound to SR10171
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / peroxisome proliferator activated receptor gamma / PPARG / nuclear receptor / inverse 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 / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / lipid homeostasis / E-box binding / alpha-actinin binding / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / 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 / 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 / intracellular receptor signaling pathway / 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 / negative regulation of miRNA transcription / peptide binding / negative regulation of angiogenesis / transcription coregulator binding / positive regulation of apoptotic signaling pathway / Regulation of PTEN gene transcription / fatty acid metabolic process / placenta development / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / mRNA transcription by RNA polymerase II / PPARA activates gene expression / regulation of circadian rhythm / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / regulation of blood pressure / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / nuclear receptor activity / rhythmic process / glucose homeostasis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / double-stranded DNA binding / DNA-binding transcription factor binding / cellular response to hypoxia / sequence-specific DNA binding / nucleic acid binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / receptor complex / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / negative regulation of gene expression / 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 / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-EKS / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.404 Å
AuthorsBruning, J.B. / Frkic, R.L.
CitationJournal: iScience / Year: 2018
Title: PPAR gamma in Complex with an Antagonist and Inverse Agonist: a Tumble and Trap Mechanism of the Activation Helix.
Authors: Frkic, R.L. / Marshall, A.C. / Blayo, A.L. / Pukala, T.L. / Kamenecka, T.M. / Griffin, P.R. / Bruning, J.B.
History
DepositionJan 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,3373
Polymers32,2551
Non-polymers1,0812
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.190, 65.190, 368.450
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 32255.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37231
#2: Chemical ChemComp-EKS / 2-{3-[(5-{[(1S)-1-(4-tert-butylphenyl)ethyl]carbamoyl}-2,3-dimethyl-1H-indol-1-yl)methyl]phenoxy}-2-methylpropanoic acid


Mass: 540.692 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H40N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.5 Å3/Da / Density % sol: 64.89 % / Description: irregular
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 4M ammonium acetate, O.1M bis-tris propane 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 12, 2016 / Details: mirrors - Si ans Rh coatings
RadiationMonochromator: Double Si with sagittaly bent second crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→73.69 Å / Num. obs: 19263 / % possible obs: 99.4 % / Redundancy: 19.4 % / Biso Wilson estimate: 50.11 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.322 / Rpim(I) all: 0.067 / Rrim(I) all: 0.33 / Net I/σ(I): 7.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 20.2 % / Rmerge(I) obs: 4.038 / Num. measured all: 39175 / Num. unique obs: 1943 / CC1/2: 0.294 / Rpim(I) all: 0.818 / Rrim(I) all: 4.132 / Net I/σ(I) obs: 0.7 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.05 Å61.41 Å
Translation7.05 Å61.41 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.25data scaling
PHASER2.6.1phasing
PHENIX1.11_2567refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4r06

4r06


Resolution: 2.404→51.296 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.4
RfactorNum. reflection% reflection
Rfree0.2768 929 4.87 %
Rwork0.2488 --
obs0.2502 19095 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 234.8 Å2 / Biso mean: 75.6543 Å2 / Biso min: 37.66 Å2
Refinement stepCycle: final / Resolution: 2.404→51.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2161 0 80 34 2275
Biso mean--67.5 55.63 -
Num. residues----278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022308
X-RAY DIFFRACTIONf_angle_d0.5593137
X-RAY DIFFRACTIONf_chiral_restr0.035351
X-RAY DIFFRACTIONf_plane_restr0.003395
X-RAY DIFFRACTIONf_dihedral_angle_d11.9671372
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4041-2.53080.3891250.37572481260698
2.5308-2.68940.36351290.35862519264899
2.6894-2.8970.39831280.32962521264999
2.897-3.18850.3271380.30792540267899
3.1885-3.64980.29861430.2632600274399
3.6498-4.59790.24321290.20752639276899
4.5979-51.30780.22131370.20332866300399
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)
16.24252.932-3.17351.1471-1.06054.20.276-0.2477-0.10470.1525-0.0561-0.17270.0040.2428-0.12780.38510.1781-0.0510.4145-0.20540.543638.1077-26.5226.7643
24.5322.0792-1.1946.7088-4.88265.4320.1724-2.01441.37141.9688-0.2052-0.1927-0.8891-1.6604-0.0421.1184-0.028-0.08141.3406-0.36460.702613.1814-33.951926.989
35.71993.7477-0.78794.93970.81712.14840.5384-0.48190.23060.2489-0.25460.0032-0.1251-0.1395-0.22140.56330.0379-0.08350.6575-0.22190.402229.0831-18.602617.546
43.45351.9963-1.39652.4826-1.47651.58430.38790.58540.3776-0.1724-0.11120.1207-0.1575-0.3447-0.20220.54350.0959-0.0020.6433-0.24630.501730.0283-16.19865.4803
59.7527-1.0446-8.20735.63691.71118.14060.8882-0.31150.58750.5581-0.47280.8607-1.2885-1.1076-0.32460.81830.0804-0.03330.6826-0.19950.530222.6132-10.42788.5281
69.6974-0.45940.81035.6161-3.80927.35990.82322.1485-0.10530.6029-0.72840.45420.8178-0.69320.12540.8154-0.042-0.26611.1067-0.19790.594722.8947-20.505233.0357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 200 through 251 )A200 - 251
2X-RAY DIFFRACTION2chain 'A' and (resid 252 through 272 )A252 - 272
3X-RAY DIFFRACTION3chain 'A' and (resid 273 through 345 )A273 - 345
4X-RAY DIFFRACTION4chain 'A' and (resid 346 through 430 )A346 - 430
5X-RAY DIFFRACTION5chain 'A' and (resid 431 through 459 )A431 - 459
6X-RAY DIFFRACTION6chain 'A' and (resid 460 through 477 )A460 - 477

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