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- PDB-6t1v: Structure of PPARg H494Y mutant in complex with GW1929 -

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Basic information

Entry
Database: PDB / ID: 6t1v
TitleStructure of PPARg H494Y mutant in complex with GW1929
Components
  • Peroxisome proliferator-activated receptor gamma
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
KeywordsTRANSCRIPTION / nuclear receptor / complex
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 / response to lipid / temperature homeostasis / response to muscle activity / lncRNA binding / negative regulation of SMAD protein signal transduction / 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 / alpha-actinin binding / intracellular glucose homeostasis / 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 / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / response to nutrient / positive regulation of gluconeogenesis / negative regulation of miRNA transcription / peptide binding / 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 / respiratory electron transport chain / gluconeogenesis / fatty acid metabolic process / mitochondrion organization / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / 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 / chromatin DNA binding / Nuclear Receptor transcription pathway
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 / : / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...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 / : / 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
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: 2.21 Å
AuthorsRochel, N.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: To Be Published
Title: Structure of a PPARg mutant complex
Authors: Rochel, N.
History
DepositionOct 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 2.0Jan 18, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / entity_src_gen / pdbx_contact_author / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_prop / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct / struct_conf / struct_mon_prot_cis / struct_site / struct_site_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_common_name / _pdbx_contact_author.id / _pdbx_entity_src_syn.organism_common_name / _pdbx_struct_assembly_prop.value / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _reflns.B_iso_Wilson_estimate / _struct.title / _struct_mon_prot_cis.pdbx_omega_angle
Description: Model completeness / Details: addition water molecules / Provider: author / Type: Coordinate replacement
Revision 2.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.accession_code

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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)33,9073
Polymers33,4122
Non-polymers4961
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-8 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.349, 120.741, 149.843
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 31888.021 Da / Num. of mol.: 1 / Mutation: H494Y
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: 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: isolated from a natural source / Formula: C30H29N3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 4 Å3/Da / Density % sol: 69.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 0.1 M Hepes pH 7.5, trisodium citrate 1.2M

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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: Sep 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.21→52.74 Å / Num. obs: 25902 / % possible obs: 99.75 % / Redundancy: 2 % / Biso Wilson estimate: 39.7 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.9
Reflection shellResolution: 2.21→2.29 Å / Num. unique obs: 2559 / CC1/2: 0.842

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xld

4xld


Resolution: 2.21→52.74 Å / SU ML: 0.2497 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.3858
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1955 2000 7.73 %
Rwork0.1662 23888 -
obs0.1685 25888 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.87 Å2
Refinement stepCycle: LAST / Resolution: 2.21→52.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2236 0 37 231 2504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00242338
X-RAY DIFFRACTIONf_angle_d0.51253154
X-RAY DIFFRACTIONf_chiral_restr0.0375364
X-RAY DIFFRACTIONf_plane_restr0.0041425
X-RAY DIFFRACTIONf_dihedral_angle_d11.2308920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.270.28651410.25611684X-RAY DIFFRACTION99.95
2.27-2.330.29561420.22791695X-RAY DIFFRACTION100
2.33-2.40.23861390.20741669X-RAY DIFFRACTION100
2.4-2.480.26421420.20931692X-RAY DIFFRACTION99.95
2.48-2.570.23441420.2021700X-RAY DIFFRACTION99.62
2.57-2.670.21151410.2021684X-RAY DIFFRACTION99.78
2.67-2.790.271420.21071685X-RAY DIFFRACTION99.84
2.79-2.940.20041390.19471675X-RAY DIFFRACTION99.73
2.94-3.120.25331430.19121694X-RAY DIFFRACTION98.6
3.12-3.360.1771410.17371700X-RAY DIFFRACTION99.95
3.36-3.70.18081440.1541715X-RAY DIFFRACTION99.95
3.7-4.230.16671440.12731717X-RAY DIFFRACTION100
4.23-5.330.14331470.12651762X-RAY DIFFRACTION100
5.34-52.740.18221530.1561816X-RAY DIFFRACTION99.34
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)
13.54814157612-1.54972889215-0.9020962977694.750180724353.9419471323.357000085310.324599249621-1.00331948218-0.5635314290491.24437450673-0.1443279465680.02463832213840.901035146155-0.1034576836160.1097243192650.643932702909-0.1291446601760.1034755408090.4658598914240.01590649086210.30275790187319.459478923641.49564529565.3763317199
22.0295685082-3.62616091334-0.8834648218237.191832091691.664844464698.01230592613-0.03429657242910.107628810712-0.7844499038150.507353559863-0.1070838502810.07429840700531.299857089210.4293759488970.2115900831320.565843785542-0.004350307527470.005652673473430.3292632123220.01688263956720.35289952019730.808003841134.055672953753.732822216
35.082067454020.7835779840111.156438784085.566452423951.335302842416.51748078961-0.00726249904215-0.55571957927-0.9742614841871.127923292730.06497870541680.4049492237190.874583441784-0.1699454228450.04337142013660.5512278393540.1462898190190.08557885306120.4275848146610.05719520700210.67268081880935.769970460826.948530499644.3215299144
42.873580253840.112073851319-4.858604594022.33623415310.8002032436848.700458687330.2823466821490.871239949854-0.805640385178-0.294170422743-0.1662717634321.780409142680.542865792937-0.4679242178760.06023956106270.4499804236080.08419770971950.004973375470220.535235778872-0.1935160704390.76469227495531.184854724826.526975123232.2017544678
56.881449661660.720750093241-0.3158260596897.32892122534-3.151176040287.866518640890.1544425622270.805247582484-0.621715351208-1.301092633830.930607689891-0.27828339764-0.118409106690.22034779849-0.7728409141840.415564351632-0.1033577287980.05985859638820.421948845285-0.1663287028210.52704176192119.729159021529.53059867930.4165609011
63.175428407180.493366619282-2.051651934623.26107488520.8744309935124.20572429414-0.1295009239410.00145561527881-0.3476845237710.00027461692272-0.1245994539040.07890771489820.3935864558810.06330071046580.2894216720330.27269531876-0.008453688155570.004769738169470.298264510802-0.06362567252640.32916679037918.557415294838.295426419542.1410025592
71.73566466510.2169492408031.232392067563.14697100006-0.4493770110261.421498763880.1750492903130.03371718368950.1902551578590.0654772670316-0.3491349511870.435705844854-0.059484723082-0.4290389190260.1867468866610.362791436421-0.03377846916440.03222335541660.435141294651-0.1204603914430.33705575865514.459557854948.498476803751.0517551573
83.07499857069-0.2857599463490.4248254701373.115432474132.450602110685.835542303760.0112347015160.17099428058-0.19967484433-0.2646286627750.0484315222585-0.249521080377-0.1924258536960.297619626941-0.03584858340140.243585012018-0.01035366132250.0427024617160.272485487206-0.00997632293640.32682436342833.344175984841.791076017240.3078662119
92.06946922705-0.7881981223651.425665417334.23867081244-0.5583023643794.31409585913-0.0912883428919-0.3309548715430.3094495314670.731705446903-0.1917529242980.0250505396681-0.246792743344-0.1395303870620.30743005750.433757543455-0.09824896541240.04450645785440.331535758879-0.07999518407460.28981922703622.029677733152.73553841160.889268375
103.8214408460.9706576948733.127910482753.121856867311.343252063842.75059421478-0.3477444944740.351095758820.337840074725-0.260669460312-0.09316800312840.167245372385-0.8078849930840.5137930307380.52182598040.3758126270370.01618294781210.01018017089340.306085345259-0.006715646343430.30454946660325.184455399853.930898202442.526303018
112.740134462211.88583519546-0.8196908652763.27584410844-2.502072647442.11496239056-0.06610958727760.775809033654-0.340665971451-0.7848081545210.07439040650950.5234047751620.489855366254-0.1850601737770.1015150203530.4750911514780.0600045977396-0.1257017519270.560692390657-0.1651103207470.38673442526114.0244229543.563970070132.8862412529
127.602788341733.649480868394.472676672742.343550995544.168394424219.72306982839-0.2549754484840.4490943439851.73917387174-1.00985568238-0.4209901775840.609964064768-1.31598254519-0.6147070908450.5880224547870.5348177788590.162617374462-0.1036302517680.58804309271-0.06818631223361.0193382423811.953234045255.571674084338.8200597409
138.433325228220.430670193218-2.010434151542.069415144590.3537926606039.784427999580.274377458671-0.2516241287090.7659861608560.0700295102864-0.3832203392111.39958443864-0.168547265243-0.5595483711440.03287872382440.348613700968-0.05691875785140.03635919064940.555944457353-0.2409749749020.6352016301113.6357616413742.782958736146.7691298138
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 238 through 253 )AA238 - 2531 - 16
22chain 'A' and (resid 254 through 267 )AA254 - 26717 - 30
33chain 'A' and (resid 268 through 279 )AA268 - 27931 - 42
44chain 'A' and (resid 280 through 289 )AA280 - 28943 - 52
55chain 'A' and (resid 290 through 304 )AA290 - 30453 - 67
66chain 'A' and (resid 305 through 330 )AA305 - 33068 - 93
77chain 'A' and (resid 331 through 361 )AA331 - 36194 - 124
88chain 'A' and (resid 362 through 405 )AA362 - 405125 - 168
99chain 'A' and (resid 406 through 458 )AA406 - 458169 - 221
1010chain 'A' and (resid 459 through 487 )AA459 - 487222 - 250
1111chain 'A' and (resid 488 through 501 )AA488 - 501251 - 264
1212chain 'A' and (resid 502 through 505 )AA502 - 505265 - 268
1313chain 'C' and (resid 141 through 150 )CD141 - 1501 - 10

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