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- PDB-6fzp: PPAR gamma complex. -

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Basic information

Entry
Database: PDB / ID: 6fzp
TitlePPAR gamma complex.
Components
  • Peroxisome proliferator-activated receptor gamma
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
KeywordsTRANSCRIPTION / nuclear receptor
Function / homology
Function and homology information


Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / cellular respiration / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / 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 ...Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / cellular respiration / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / 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 / response to starvation / temperature homeostasis / positive regulation of fatty acid metabolic process / STAT family protein binding / response to lipid / lncRNA binding / response to muscle activity / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / intracellular glucose homeostasis / negative regulation of SMAD protein signal transduction / fatty acid oxidation / response to dietary excess / lipid homeostasis / E-box binding / alpha-actinin binding / R-SMAD binding / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of blood vessel endothelial cell migration / monocyte differentiation / white fat cell differentiation / cellular response to low-density lipoprotein particle stimulus / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / cell fate commitment / adipose tissue development / negative regulation of osteoblast differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / BMP signaling pathway / long-chain fatty acid transport / brown fat cell differentiation / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / energy homeostasis / cell maturation / digestion / negative regulation of MAPK cascade / intracellular receptor signaling pathway / hormone-mediated signaling pathway / positive regulation of adipose tissue development / response to nutrient / peroxisome proliferator activated receptor signaling pathway / epithelial cell differentiation / positive regulation of gluconeogenesis / regulation of cellular response to insulin stimulus / peptide binding / SUMOylation of transcription cofactors / RNA splicing / negative regulation of miRNA transcription / negative regulation of angiogenesis / placenta development / Regulation of PTEN gene transcription / nuclear receptor binding / positive regulation of apoptotic signaling pathway / transcription coregulator binding / gluconeogenesis / respiratory electron transport chain / transcription coregulator activity / mitochondrion organization / transcription initiation at RNA polymerase II promoter / SUMOylation of intracellular receptors / circadian regulation of gene expression / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / fatty acid metabolic process / regulation of circadian rhythm / PML body / chromatin DNA binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation
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-EDK / 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: 2.3 Å
AuthorsRochel, N. / Beji, S.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Nat Commun / Year: 2019
Title: Recurrent activating mutations of PPAR gamma associated with luminal bladder tumors.
Authors: Rochel, N. / Krucker, C. / Coutos-Thevenot, L. / Osz, J. / Zhang, R. / Guyon, E. / Zita, W. / Vanthong, S. / Hernandez, O.A. / Bourguet, M. / Badawy, K.A. / Dufour, F. / Peluso-Iltis, C. / ...Authors: Rochel, N. / Krucker, C. / Coutos-Thevenot, L. / Osz, J. / Zhang, R. / Guyon, E. / Zita, W. / Vanthong, S. / Hernandez, O.A. / Bourguet, M. / Badawy, K.A. / Dufour, F. / Peluso-Iltis, C. / Heckler-Beji, S. / Dejaegere, A. / Kamoun, A. / de Reynies, A. / Neuzillet, Y. / Rebouissou, S. / Beraud, C. / Lang, H. / Massfelder, T. / Allory, Y. / Cianferani, S. / Stote, R.H. / Radvanyi, F. / Bernard-Pierrot, I.
History
DepositionMar 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 2.0Apr 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / diffrn / entity / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn.pdbx_serial_crystal_experiment / _entity_src_gen.gene_src_common_name / _pdbx_contact_author.id / _pdbx_entity_src_syn.organism_common_name / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_percent_reflns_obs / _refine.pdbx_ls_cross_valid_method / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_redundancy / _reflns.percent_possible_obs / _reflns_shell.d_res_low / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _software.version
Description: Atoms with unrealistic or zero occupancies / Details: addition of water molecules removal of Na / Provider: author / Type: Coordinate replacement
Revision 2.1May 4, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 2.2Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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


Theoretical massNumber of molelcules
Total (without water)33,4693
Polymers32,9732
Non-polymers4961
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-11 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.592, 86.268, 122.693
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P37231
#2: Protein/peptide Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / PPARGC-1-alpha / Ligand effect modulator 6


Mass: 1523.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2
#3: Chemical ChemComp-EDK / (2~{S})-3-[4-[2-[methyl(pyridin-2-yl)amino]ethoxy]phenyl]-2-[[2-(phenylcarbonyl)phenyl]amino]propanoic acid


Mass: 495.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H29N3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NH4 acetate 0.3M, Hepes 0.1M pH 7.5, di-sodium tartrate 0.8 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.968 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.3→17.32 Å / Num. obs: 12556 / % possible obs: 96.6 % / Redundancy: 2 % / Rmerge(I) obs: 0.016 / Net I/σ(I): 19.73
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 1238 / CC1/2: 0.914

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PRG

1prg


Resolution: 2.3→17.32 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 33.09
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1164 9.27 %random
Rwork0.219 11392 --
obs0.219 12556 96.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.18 Å2 / Biso mean: 83.201 Å2 / Biso min: 35.19 Å2
Refinement stepCycle: final / Resolution: 2.3→17.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 37 64 2239
Biso mean--73.55 72.21 -
Num. residues----267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.40440.40561420.3291429157198
2.4044-2.53080.34661350.29541433156898
2.5308-2.68890.30951490.29321418156798
2.6889-2.89560.33541490.26621420156999
2.8956-3.18530.33361440.2751388153294
3.1853-3.64250.24731390.22551323146291
3.6425-4.57520.2131470.18241477162499
4.5752-17.31820.22361590.18631504166397
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)
17.148-1.4259-2.92679.48826.70375.29010.75650.02520.9216-0.0945-0.1224-0.5095-0.8239-0.1805-0.87041.1793-0.22120.23940.81320.11280.8381-18.60958.080613.2102
25.80342.86551.14186.34854.89355.71230.00780.6764-0.3819-0.9469-0.00890.1563-0.2963-0.1978-0.00440.9088-0.0747-0.08151.0275-0.05840.5784-30.9867-15.6213-0.0369
34.0950.4124-0.71674.17471.55394.9905-0.1622-0.0567-0.37780.0410.4963-0.750.29391.1934-0.34870.53860.1225-0.02650.7307-0.12390.491-15.2455-11.469613.7678
46.0136-0.90781.28098.53472.16754.6284-0.23660.2667-0.76570.47030.17140.5331.3029-0.5840.09180.6741-0.18180.01620.4876-0.04810.4553-32.512-18.669512.1293
57.9818-1.45361.10466.7050.77488.05620.1022-0.10250.6409-0.14230.3318-0.3799-0.39671.0151-0.3610.5541-0.14110.04140.6115-0.13950.3798-20.66121.965823.1838
66.8477-5.4011-4.07754.99134.43673.6948-0.7244-0.7918-1.04121.52030.49890.82911.24410.51080.1140.9320.1221-0.05320.73050.0950.5362-24.1515-15.622524.1771
79.1105-4.2352-5.04868.44571.17715.8201-0.094-0.7969-0.27130.35550.644-0.65431.14170.8984-0.63650.90490.2316-0.12971.07550.13750.6963-12.7608-24.870216.6476
81.75142.59322.91173.79664.18434.81460.823-0.74431.97140.68880.5861-0.64441.34791.4927-0.85580.7244-0.01430.25421.1711-0.09211.0477-2.995-11.202812.4511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 207 THROUGH 225 )A0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 226 THROUGH 276 )A0
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 277 THROUGH 333 )A0
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 334 THROUGH 377 )A0
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 378 THROUGH 430 )A0
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 431 THROUGH 458 )A0
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 459 THROUGH 477 )A0
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 142 THROUGH 150 )C0

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