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- PDB-6t1s: PPAR mutant -

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Basic information

Entry
Database: PDB / ID: 6t1s
TitlePPAR mutant
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / nuclear receptor / transcrption factor / complex / NUCLEAR PROTEIN
Function / homology
Function and homology information


prostaglandin receptor activity / regulation of cholesterol transporter 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 / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonate binding ...prostaglandin receptor activity / regulation of cholesterol transporter 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 / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonate binding / positive regulation of low-density lipoprotein receptor activity / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / DNA binding domain binding / macrophage derived foam cell differentiation / STAT family protein binding / positive regulation of vascular associated smooth muscle cell apoptotic process / 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 macrophage derived foam cell differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / white fat cell differentiation / negative regulation of BMP signaling pathway / negative regulation of mitochondrial fission / positive regulation of cholesterol efflux / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / retinoic acid receptor signaling pathway / cell fate commitment / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cell maturation / negative regulation of signaling receptor activity / epithelial cell differentiation / 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 / negative regulation of MAP kinase activity / fatty acid metabolic process / Regulation of PTEN gene transcription / transcription coregulator binding / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / peptide binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / placenta development / regulation of circadian rhythm / PPARA activates gene expression / lipid metabolic process / positive regulation of DNA-binding transcription factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of blood pressure / negative regulation of inflammatory response / positive regulation of miRNA transcription / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / activation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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-EDK / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRochel, N.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: To Be Published
Title: Structure of PPARg mutant
Authors: Rochel, N.
History
DepositionOct 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4914
Polymers31,8031
Non-polymers6883
Water4,234235
1
A: Peroxisome proliferator-activated receptor gamma
hetero molecules

A: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9818
Polymers63,6062
Non-polymers1,3756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2640 Å2
ΔGint-56 kcal/mol
Surface area25890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.660, 60.660, 169.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-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: 31802.896 Da / Num. of mol.: 1 / Mutation: F310S
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: 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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 25% PEG3350, 0.2 M LiSO4, BisTris 0.1M pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.646→49.33 Å / Num. obs: 39355 / % possible obs: 99.72 % / Redundancy: 2 % / Biso Wilson estimate: 33.72 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.00959 / Rpim(I) all: 0.00959 / Net I/σ(I): 25.75
Reflection shellResolution: 1.646→1.705 Å / Mean I/σ(I) obs: 0.95 / Num. unique obs: 3818 / CC1/2: 0.524

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XLD

4xld


Resolution: 1.65→49.33 Å / SU ML: 0.2225 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9409
RfactorNum. reflection% reflection
Rfree0.2044 1993 5.08 %
Rwork0.1709 --
obs0.1726 39253 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.32 Å2
Refinement stepCycle: LAST / Resolution: 1.65→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 47 235 2481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01062326
X-RAY DIFFRACTIONf_angle_d1.15053144
X-RAY DIFFRACTIONf_chiral_restr0.0518359
X-RAY DIFFRACTIONf_plane_restr0.007428
X-RAY DIFFRACTIONf_dihedral_angle_d13.53581451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.33331350.31132527X-RAY DIFFRACTION96.27
1.69-1.730.2951390.28292597X-RAY DIFFRACTION100
1.73-1.780.3661410.28762646X-RAY DIFFRACTION100
1.78-1.840.30341400.25152610X-RAY DIFFRACTION100
1.84-1.910.25981390.21462601X-RAY DIFFRACTION100
1.91-1.980.23061400.19132621X-RAY DIFFRACTION100
1.98-2.070.21641420.17782633X-RAY DIFFRACTION100
2.07-2.180.18831410.16832649X-RAY DIFFRACTION100
2.18-2.320.20021420.16352666X-RAY DIFFRACTION100
2.32-2.50.1861430.16372658X-RAY DIFFRACTION100
2.5-2.750.19981440.16782684X-RAY DIFFRACTION100
2.75-3.150.2191440.17932704X-RAY DIFFRACTION100
3.15-3.970.21571470.16382743X-RAY DIFFRACTION100
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)
12.28078574839-2.422891558021.010575575356.79716043542-2.647413759244.110136784630.116644259162-0.0115271209172-0.190750437657-0.289779169573-0.1173939701580.2263060640510.397945947543-0.223666347532-0.1016000612890.360966339206-0.0853581798996-0.02289843690250.248300953331-0.04686384165420.2586130669269.66806280599-24.010489036826.6079690782
28.565026301280.851787129743-2.029612732222.784860335453.042435995326.807364215260.01902142818510.489753960622-0.376194624614-1.23963901994-0.4932954872290.7855460698420.410317414424-0.3653165331590.4213478811140.5472109093960.0116965217391-0.0605034425590.4787689917810.01099839944470.3793234330772.73421432323-0.01990299734927.3963782883
34.208185320813.418809418161.54986028243.35337276355-0.4004609081477.02193672285-0.148434002205-0.150464971296-1.7188431105-0.807391051653-0.1122901750541.547126985120.741651588241-0.8238215151160.2326340049510.6860593551240.132799655768-0.08012844600260.9764712887940.0497857549281.38548082906-12.41068208183.88156264410.7263589213
43.88341181018-2.437630626192.880122478541.88659312668-2.344863567574.719843567860.145995248546-0.0268780125021-0.0656090453807-0.7492678612530.2380659683941.014715859170.302352867545-0.612419894219-0.7505320583780.229331748002-0.017099453484-0.01995340397320.468153136595-0.02262659017090.465063761007-7.59188113898-5.8111430374421.1158398899
53.99502239080.607065387142-0.6195657886083.79128813523-1.36661500062.544727043370.0977137257287-0.256955667546-0.2476077645080.231006384256-0.04050582625770.5972287085810.170351770846-0.656835837348-0.032378071530.231202668587-0.1112439487790.01747412587850.382174743812-0.004056948241180.333293100957-4.22477037962-15.370472174734.0768317426
67.31401266319-1.16326734414-1.893119790174.50763213531-0.3629980630473.615950315560.280781391145-0.008525837312780.2128004272210.159804678192-0.1775339629050.3687419979660.0264944667256-0.590066142513-0.00642242696020.2858419638740.00898105608623-0.0274959035040.3513462762480.03691392672980.2840842840542.046470418463.2492876282818.3419470847
74.72381369489-5.075546660816.353905871315.443239553-6.884965815679.01736740003-0.340848576293-0.2792340946110.2970476439880.3937789240930.115142381999-0.316440014563-0.42392562329-0.2361250817810.2130189217640.278573238366-0.0247192511314-0.004617814597460.282952116036-0.01123221746540.3183697526119.83004214902-1.8646114802627.5749400879
84.51357737877-0.565364000613-1.474596026862.17897396786-0.06636122058323.753504733080.0422237473955-0.213603114536-0.07279689216690.143965623098-0.02966435772750.1840593853520.192054370352-0.2051297879460.03426304381890.275707151591-0.0750864399667-0.01033177541340.240148062056-0.006317662175390.247621854328.10009870869-18.751266143136.9301442751
93.4966796111-0.6807967895853.651105516862.29686521384-2.905580402925.76755669624-0.360068193533-0.6335078837990.5417577739320.5103935691170.4208272101630.249928884353-0.52537752598-0.804962422244-0.05372856487550.2686622731870.003847713428230.05553991480030.348814776334-0.0003774930089440.3450782258751.01819234462-1.4719556659835.0180784222
106.480075297931.44360093762.25182207275.64423531710.1015070712319.63966048048-0.2459064037220.7243593220070.292869712030.2649028454140.03639118883521.74783739319-1.15129725915-1.50608841447-0.179186271770.1803453683930.150306950527-0.01627434342970.7998487825590.01912325128770.798630126396-14.3407901642-2.5566023740330.7676043489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 230 through 265 )
2X-RAY DIFFRACTION2chain 'A' and (resid 266 through 285 )
3X-RAY DIFFRACTION3chain 'A' and (resid 286 through 300 )
4X-RAY DIFFRACTION4chain 'A' and (resid 301 through 330 )
5X-RAY DIFFRACTION5chain 'A' and (resid 331 through 361 )
6X-RAY DIFFRACTION6chain 'A' and (resid 362 through 392 )
7X-RAY DIFFRACTION7chain 'A' and (resid 393 through 405 )
8X-RAY DIFFRACTION8chain 'A' and (resid 406 through 458 )
9X-RAY DIFFRACTION9chain 'A' and (resid 459 through 487 )
10X-RAY DIFFRACTION10chain 'A' and (resid 488 through 505 )

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