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- PDB-4r2u: Crystal Structure of PPARgamma in complex with SR1664 -

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Basic information

Entry
Database: PDB / ID: 4r2u
TitleCrystal Structure of PPARgamma in complex with SR1664
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / nuclear receptor ligand binding domain
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 / arachidonic acid 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 / arachidonic acid binding / positive regulation of low-density lipoprotein receptor activity / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / positive regulation of vascular associated smooth muscle cell apoptotic process / macrophage derived foam cell differentiation / DNA binding 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 / negative regulation of blood vessel endothelial cell migration / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / positive regulation of cholesterol efflux / negative regulation of macrophage derived foam cell differentiation / cellular response to low-density lipoprotein particle stimulus / negative regulation of lipid storage / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / long-chain fatty acid transport / retinoic acid receptor signaling pathway / positive regulation of DNA binding / cell fate commitment / BMP signaling pathway / nuclear retinoid X receptor binding / negative regulation of signaling receptor activity / regulation of cellular response to insulin stimulus / cell maturation / positive regulation of adipose tissue development / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / negative regulation of angiogenesis / response to nutrient / negative regulation of MAP kinase activity / fatty acid metabolic process / negative regulation of miRNA transcription / placenta development / Regulation of PTEN gene transcription / negative regulation of smooth muscle cell proliferation / transcription coregulator binding / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / lipid metabolic process / regulation of circadian rhythm / PPARA activates gene expression / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of blood pressure / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / 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 / : / rhythmic process / nuclear receptor activity / positive regulation of DNA-binding transcription factor activity / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / innate immune response / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding
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 / Zinc finger, C4 type (two domains) ...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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-3JX / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsMarciano, D.P. / Kamenecka, T. / Griffin, P.R. / Bruning, J.B.
CitationJournal: Nat Commun / Year: 2015
Title: Pharmacological repression of PPAR gamma promotes osteogenesis.
Authors: Marciano, D.P. / Kuruvilla, D.S. / Boregowda, S.V. / Asteian, A. / Hughes, T.S. / Garcia-Ordonez, R. / Corzo, C.A. / Khan, T.M. / Novick, S.J. / Park, H. / Kojetin, D.J. / Phinney, D.G. / ...Authors: Marciano, D.P. / Kuruvilla, D.S. / Boregowda, S.V. / Asteian, A. / Hughes, T.S. / Garcia-Ordonez, R. / Corzo, C.A. / Khan, T.M. / Novick, S.J. / Park, H. / Kojetin, D.J. / Phinney, D.G. / Bruning, J.B. / Kamenecka, T.M. / Griffin, P.R.
History
DepositionAug 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
D: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9944
Polymers62,8992
Non-polymers1,0952
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peroxisome proliferator-activated receptor gamma
hetero molecules

D: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9944
Polymers62,8992
Non-polymers1,0952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555x+1/2,y+1/2,z1
Buried area2060 Å2
ΔGint-11 kcal/mol
Surface area23660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.630, 63.670, 118.930
Angle α, β, γ (deg.)90.000, 103.430, 90.000
Int Tables number5
Space group name H-MC121

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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 / Fragment: UNP residues 231-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1C3, PPARG / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37231
#2: Chemical ChemComp-3JX / 4'-[(2,3-dimethyl-5-{[(1S)-1-(4-nitrophenyl)ethyl]carbamoyl}-1H-indol-1-yl)methyl]biphenyl-2-carboxylic acid


Mass: 547.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H29N3O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1uL protein-ligand complex solution (10mg/mL) was mixed with 1uL well solution (2M ammonium sulfate and 0.1M Tris 8.0), VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2011 / Details: mirrors
RadiationMonochromator: single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.3→41.34 Å / Num. all: 28278 / Num. obs: 28278 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.74 % / Biso Wilson estimate: 44.62 Å2 / Rmerge(I) obs: 0.094 / Χ2: 1 / Net I/σ(I): 6.2 / Scaling rejects: 800
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.3-2.383.480.5321.7806223021.2879.4
2.38-2.483.740.5131.91067228221.2698.2
2.48-2.593.790.46521093328551.1698.7
2.59-2.733.80.3982.21093028701.1398.8
2.73-2.93.790.30631101828921.0998.9
2.9-3.123.770.2343.91080428461.0399.2
3.12-3.443.770.145.91102529050.8899.2
3.44-3.933.770.0839.61104929090.7899.3
3.93-4.953.770.0613.51107429160.7399.4
4.95-41.343.690.04517.11104729610.7698.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.9Ldata reduction
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.14data extraction
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q59

2q59


Resolution: 2.3→31.474 Å / SU ML: 0.31 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 27.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1419 5.08 %random
Rwork0.189 ---
obs0.192 27958 95.44 %-
all-27958 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.81 Å2 / Biso mean: 53.6378 Å2 / Biso min: 24.48 Å2
Refinement stepCycle: LAST / Resolution: 2.3→31.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4013 0 82 173 4268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054175
X-RAY DIFFRACTIONf_angle_d1.0385647
X-RAY DIFFRACTIONf_chiral_restr0.037653
X-RAY DIFFRACTIONf_plane_restr0.004715
X-RAY DIFFRACTIONf_dihedral_angle_d15.5271553
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.37780.348830.30412000208372
2.3778-2.4730.34211500.28542631278195
2.473-2.58550.29611450.25842677282298
2.5855-2.72170.29251450.2412723286898
2.7217-2.89210.24451310.21622767289898
2.8921-3.11530.28141380.20932709284798
3.1153-3.42840.27661470.19062753290098
3.4284-3.92370.21021290.15952772290198
3.9237-4.94040.20681640.14762722288698
4.9404-31.47670.2461870.182785297298
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)
12.82960.5492-1.00251.39761.16163.9028-0.3776-0.2783-0.08910.1490.3537-0.14650.21690.54710.03330.27570.028-0.0310.2710.00260.343431.1894-0.663942.7698
24.3485-0.317-0.55194.57170.43924.34750.5003-0.5586-0.58110.1688-0.458-0.98280.05030.320.06680.27650.0094-0.01610.46370.10610.565917.920411.766261.1198
32.9791-0.9046-2.29051.9886-0.25213.18180.10870.09920.39060.0566-0.04190.0409-0.4925-0.1639-0.13430.29080.0078-0.05370.2792-0.01910.303419.202312.958339.3992
42.8029-1.80820.83012.78620.38473.7612-0.02270.5478-0.24580.02110.01660.2324-0.3879-0.6301-0.00860.35010.05640.03170.4971-0.02650.33319.11311.757751.4996
51.569-0.1148-0.61491.46620.52922.2532-0.03330.1616-0.16090.0103-0.1240.03460.0257-0.13790.17220.28080.0095-0.02780.3136-0.03940.398817.9004-0.719437.8641
61.5535-0.27540.75484.5947-0.63154.5152-0.02850.0349-0.4266-0.38230.09240.05320.9753-0.23670.03650.2868-0.00240.03020.3106-0.08140.463826.1075-9.854733.0342
71.8357-0.7101-0.30181.28930.00431.70740.10940.4762-0.0369-0.3576-0.020.3185-0.0785-0.3603-0.07960.33130.0026-0.03560.5034-0.04330.40149.86128.59334.7122
82.0443-0.2709-0.4094.05260.33293.52550.0350.3942-0.2414-0.24470.0392-0.44780.49050.2656-0.120.44720.01490.04420.3717-0.13820.46269.6981-29.982623.4201
92.36121.6984-0.20671.187-0.08753.6480.4680.7028-0.4827-0.3475-0.49520.00060.1787-0.39190.06840.76690.0878-0.01280.99890.06640.35510.9162-22.14652.6125
102.89480.444-2.08130.06160.20495.272-0.06091.5357-0.0604-0.6167-0.14150.537-0.0953-0.89650.08110.83190.0093-0.06731.09430.00940.5549-12.8312-17.07556.8868
111.7211-0.70440.24421.7297-1.12732.97830.09150.1018-0.1695-0.13270.04270.0852-0.1632-0.2024-0.11480.3423-0.02770.02470.3145-0.03990.3196-2.3303-20.201729.203
122.6188-0.87980.73381.1442-0.2743.5091-0.08390.05940.3233-0.30130.0617-0.011-0.814-0.16350.0520.73030.00360.0920.4779-0.01280.36752.4295-11.019413.3485
132.62271.22410.66541.8456-0.14723.33020.00880.1652-0.3746-0.16580.0988-0.4575-0.0520.6343-0.15560.3082-0.0168-0.01650.301-0.09010.399113.6512-21.886234.1391
145.2037-1.6596-0.3162.66990.9762.65740.33710.10430.3424-0.4502-0.20620.2076-0.78-0.3181-0.11980.572-0.0451-0.03590.4568-0.04530.35077.2264-8.883428.0853
152.4030.5183-0.36371.86320.2660.9429-0.02280.23040.63880.6460.25550.4927-0.5811-0.2272-0.13250.66450.02940.12710.61640.03380.669-17.2547-11.506226.1357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 205 through 237 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 238 through 251 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 252 through 333 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 334 through 364 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 365 through 402 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 403 through 427 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 428 through 476 )A0
8X-RAY DIFFRACTION8chain 'D' and (resid 208 through 238 )D0
9X-RAY DIFFRACTION9chain 'D' and (resid 239 through 251 )D0
10X-RAY DIFFRACTION10chain 'D' and (resid 252 through 276 )D0
11X-RAY DIFFRACTION11chain 'D' and (resid 277 through 333 )D0
12X-RAY DIFFRACTION12chain 'D' and (resid 334 through 377 )D0
13X-RAY DIFFRACTION13chain 'D' and (resid 378 through 430 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 431 through 456 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 457 through 475 )D0

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