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- PDB-4r6s: Crystal structure of PPARgammma in complex with SR1663 -

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Basic information

Entry
Database: PDB / ID: 4r6s
TitleCrystal structure of PPARgammma in complex with SR1663
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 / DNA binding domain binding / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / 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 / 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 / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / cell fate commitment / positive regulation of DNA binding / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / regulation of cellular response to insulin stimulus / 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 / 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 / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / placenta development / regulation of circadian rhythm / lipid metabolic process / PPARA activates gene expression / regulation of blood pressure / positive regulation of DNA-binding transcription factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / nuclear receptor activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / : / 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 / 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 / intracellular membrane-bounded organelle / innate immune response / 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-3K2 / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.301 Å
AuthorsMarciano, D.P. / 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 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
B: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0864
Polymers62,9912
Non-polymers1,0952
Water2,090116
1


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

B: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0864
Polymers62,9912
Non-polymers1,0952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area1850 Å2
ΔGint-12 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.241, 61.940, 119.226
Angle α, β, γ (deg.)90.00, 103.44, 90.00
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: 31495.590 Da / Num. of mol.: 2 / Fragment: UNP residues 231-505 / Mutation: T447F
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-3K2 / 4'-[(2,3-dimethyl-5-{[(1R)-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


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.4M sodium citrate, 0.125M Tris 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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→50 Å / Num. all: 28903 / Num. obs: 28903 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 57.99 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.3-2.344.20.426198.1
2.34-2.384.20.362197.7
2.38-2.434.10.291196.3
2.43-2.483.90.251195.1
2.48-2.533.60.226194.5
2.53-2.594.30.202198.6
2.59-2.664.40.155199.5
2.66-2.734.40.131199.2
2.73-2.814.40.11199.5
2.81-2.94.30.091199.6
2.9-34.30.08199.6
3-3.124.30.066198.2
3.12-3.264.30.049198.4
3.26-3.444.20.042196.4
3.44-3.653.70.036192.6
3.65-3.934.20.034198.6
3.93-4.334.40.031199.7
4.33-4.954.30.028199.7
4.95-6.244.10.026198.1
6.24-5040.016196.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.3 Å41.12 Å
Translation2.3 Å41.12 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.1phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q59

2q59


Resolution: 2.301→41.124 Å / SU ML: 0.23 / Isotropic thermal model: isotropic / σ(F): 1.36 / Phase error: 24.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 1452 5.03 %
Rwork0.171 --
obs0.174 28889 97.64 %
all-28889 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.57 Å2
Refinement stepCycle: LAST / Resolution: 2.301→41.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4011 0 82 116 4209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094229
X-RAY DIFFRACTIONf_angle_d1.1165741
X-RAY DIFFRACTIONf_dihedral_angle_d14.6591570
X-RAY DIFFRACTIONf_chiral_restr0.069663
X-RAY DIFFRACTIONf_plane_restr0.004734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.301-2.38320.27921290.20222703X-RAY DIFFRACTION97
2.3832-2.47860.26031410.18852674X-RAY DIFFRACTION96
2.4786-2.59140.24771390.18912686X-RAY DIFFRACTION96
2.5914-2.7280.2291440.17662772X-RAY DIFFRACTION99
2.728-2.89890.24591600.17652770X-RAY DIFFRACTION99
2.8989-3.12270.28451530.19572788X-RAY DIFFRACTION99
3.1227-3.43680.25051570.18162706X-RAY DIFFRACTION97
3.4368-3.93370.21471330.16122689X-RAY DIFFRACTION96
3.9337-4.95480.21421590.15152811X-RAY DIFFRACTION100
4.9548-41.13090.22851370.17462838X-RAY DIFFRACTION97
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)
10.4616-0.160.21450.05930.1030.5961-0.34210.0607-0.12580.23070.3240.1440.0087-0.88330.00030.57720.06870.08120.78430.08590.69488.573346.024320.3033
20.4095-0.34940.52020.1953-0.26210.3972-0.31191.1234-0.5376-0.04990.23880.1577-0.2385-0.3048-0.00080.5946-0.01260.02610.742-0.02690.5594102.001259.25311.273
30.33931.36890.10281.08970.30390.6359-0.2673-0.18190.2241-0.01870.23570.0338-0.16550.2710.00040.66090.106-0.08470.61530.04740.6285104.976164.166719.113
40.41080.8013-0.36220.8153-0.4340.9376-0.09650.0071-0.14970.05370.0046-0.1293-0.3050.7373-0.00010.65220.01130.02780.9478-0.01010.6151115.022559.81727.6371
50.79790.70980.43081.7356-0.0920.4785-0.0221-0.1649-0.38820.06510.1488-0.05360.47760.2329-0.00010.56280.1945-0.02240.60710.03620.608799.764945.536824.3184
60.58180.4365-0.394-0.0237-0.0895-0.06860.048-0.5916-0.26040.4610.0827-0.70160.19710.45210.00070.6910.1789-0.10110.7749-0.02680.8745115.75653.856721.5969
70.24520.17070.20960.09090.09990.08610.8708-0.78531.36741.0869-0.6327-0.3868-1.20610.39570.00071.0728-0.01650.00271.04210.03790.8078114.176371.335825.6304
80.0788-0.08540.02620.0048-0.02420.06350.14740.611-0.8639-0.0834-0.20160.05250.53850.3793-0.0010.81420.0984-0.00820.44820.03220.8694113.250419.833327.2607
90.0408-0.01850.02710.0495-0.14690.15570.4271-0.6884-0.75520.0555-0.11120.09220.6110.83540.00140.98140.1910.00140.95720.13810.6433122.298429.401248.513
10-0.01570.0175-0.01420.00110.02450.02010.5296-1.91920.2930.4577-0.18550.78360.40470.4875-0.00230.93680.0665-0.07081.2794-0.03030.911139.087436.425552.1375
110.2589-0.1264-0.08690.04270.23720.1560.0741-0.6042-0.25680.0016-0.08610.0497-0.0179-0.15670.00010.60830.15610.04210.6479-0.03180.5331133.186633.552835.3465
121.1373-0.36370.31410.20420.07290.2277-0.1230.2538-0.0130.06110.1522-0.0120.00750.2021-0.00040.58340.10960.04790.5523-0.00660.6108125.0332.422923.0643
130.78840.76980.23790.23420.05490.40820.0279-0.67790.05680.38410.12080.1265-0.68020.0614-0.00050.94060.15320.04320.8015-0.02470.6088124.159442.128144.7237
141.9504-0.65420.36531.63660.31451.8484-0.0094-0.0672-0.0184-0.01910.00780.3744-0.2546-0.226200.52520.1419-0.01990.49710.03340.5968113.853235.180625.7431
150.08840.0578-0.07990.1374-0.1594-0.0204-0.23310.8672-0.39830.3443-0.1403-0.39970.78891.9313-0.00010.9333-0.11840.17381.4210.06791.1489142.801944.088532.9739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 203 through 225 )
2X-RAY DIFFRACTION2chain 'A' and (resid 226 through 251 )
3X-RAY DIFFRACTION3chain 'A' and (resid 252 through 333 )
4X-RAY DIFFRACTION4chain 'A' and (resid 334 through 377 )
5X-RAY DIFFRACTION5chain 'A' and (resid 378 through 430 )
6X-RAY DIFFRACTION6chain 'A' and (resid 431 through 459 )
7X-RAY DIFFRACTION7chain 'A' and (resid 460 through 476 )
8X-RAY DIFFRACTION8chain 'B' and (resid 207 through 225 )
9X-RAY DIFFRACTION9chain 'B' and (resid 226 through 251 )
10X-RAY DIFFRACTION10chain 'B' and (resid 252 through 276 )
11X-RAY DIFFRACTION11chain 'B' and (resid 277 through 302 )
12X-RAY DIFFRACTION12chain 'B' and (resid 303 through 333 )
13X-RAY DIFFRACTION13chain 'B' and (resid 334 through 377 )
14X-RAY DIFFRACTION14chain 'B' and (resid 378 through 453 )
15X-RAY DIFFRACTION15chain 'B' and (resid 454 through 474 )

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