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- PDB-4r06: Crystal Structure of SR2067 bound to PPARgamma -

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Basic information

Entry
Database: PDB / ID: 4r06
TitleCrystal Structure of SR2067 bound to PPARgamma
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / nuclear receptor / ligand binding protein
Function / homology
Function and homology information


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 ...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 / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / lipid homeostasis / E-box binding / alpha-actinin binding / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / 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 / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cell maturation / intracellular receptor signaling pathway / positive regulation of adipose tissue development / hormone-mediated signaling pathway / peroxisome proliferator activated receptor signaling pathway / epithelial cell differentiation / regulation of cellular response to insulin stimulus / response to nutrient / negative regulation of miRNA transcription / peptide binding / negative regulation of angiogenesis / transcription coregulator binding / positive regulation of apoptotic signaling pathway / Regulation of PTEN gene transcription / fatty acid metabolic process / placenta development / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / mRNA transcription by RNA polymerase II / PPARA activates gene expression / regulation of circadian rhythm / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / regulation of blood pressure / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / nuclear receptor activity / rhythmic process / glucose homeostasis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / double-stranded DNA binding / DNA-binding transcription factor binding / cellular response to hypoxia / sequence-specific DNA binding / nucleic acid binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / receptor complex / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / negative regulation of gene expression / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II
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 ...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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-3E7 / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 Å
AuthorsMarrewijk, L. / Kamenecka, T. / Griffin, P.R. / Bruning, J.B.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: SR2067 Reveals a Unique Kinetic and Structural Signature for PPAR gamma Partial Agonism.
Authors: van Marrewijk, L.M. / Polyak, S.W. / Hijnen, M. / Kuruvilla, D. / Chang, M.R. / Shin, Y. / Kamenecka, T.M. / Griffin, P.R. / Bruning, J.B.
History
DepositionJul 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: 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
B: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9814
Polymers62,4162
Non-polymers5652
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.790, 62.600, 118.570
Angle α, β, γ (deg.)90.000, 101.930, 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: 31208.236 Da / Num. of mol.: 2 / Fragment: UNP residues 233-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1C3, PPARG, PPARG_HUMAN / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37231
#2: Chemical ChemComp-3E7 / 1-(naphthalen-1-ylsulfonyl)-N-[(1S)-1-phenylpropyl]-1H-indole-5-carboxamide


Mass: 468.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H24N2O3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein ligand complex at 10mg/mL in 20mM Tris 8.0, 10mM NaCl, 1mM TCEP mixed with equal volume of well solution of 2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2011 / Details: mirrors
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionRedundancy: 3.6 % / Number: 108199 / Rmerge(I) obs: 0.075 / D res high: 2.22 Å / D res low: 39.98 Å / Num. obs: 30423 / % possible obs: 92.3 / Rejects: 16
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
2.222.2911.0853.6
8.8839.9810.0243.8
ReflectionResolution: 2.22→39.98 Å / Num. obs: 30423 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 46.47 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 9.9 / Scaling rejects: 16
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique all% possible all
2.22-2.293.61.310134285495.5
8.88-39.983.877.2170345481

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.22 Å39.98 Å
Translation2.22 Å39.98 Å

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Processing

Software
NameVersionClassificationNB
Aimless0.2.8data scaling
PHASER2.5.1phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q6R

2q6r


Resolution: 2.22→39.98 Å / FOM work R set: 0.7788 / SU ML: 0.31 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 29.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1534 5.05 %random
Rwork0.186 ---
all0.1888 ---
obs0.1888 30388 91.81 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 441.7 Å2 / Biso mean: 67.15 Å2 / Biso min: 26.51 Å2
Refinement stepCycle: LAST / Resolution: 2.22→39.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4015 0 39 178 4232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084206
X-RAY DIFFRACTIONf_angle_d1.1275694
X-RAY DIFFRACTIONf_chiral_restr0.077662
X-RAY DIFFRACTIONf_plane_restr0.005718
X-RAY DIFFRACTIONf_dihedral_angle_d17.0161605
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.22-2.29170.33351310.29432665279695
2.2917-2.37360.37591410.28862712285395
2.3736-2.46860.32051570.2692646280394
2.4686-2.58090.32891310.25352476260786
2.5809-2.7170.32971500.23652684283495
2.717-2.88710.28511290.21132712284195
2.8871-3.110.31621270.20782579270689
3.11-3.42280.26521300.18162587271792
3.4228-3.91770.20081270.15242706283393
3.9177-4.93450.19541410.1412570271190
4.9345-39.980.19761700.17562517268786
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)
10.1514-0.10120.11770.21030.230.3935-0.14560.0124-0.0328-0.06790.26120.2261-0.2194-0.3896-0.0070.32150.05230.0370.47090.08070.3995-0.124416.28415.0081
22.5741-0.9144-0.12791.50980.05780.00730.2660.814-0.4851-0.0353-0.14390.2636-0.68640.29070.14140.5642-0.22620.02460.5789-0.03190.126114.889832.0212-3.3064
30.20840.4599-0.10270.6296-0.1350.7465-0.24250.0578-0.18130.0430.1125-0.0411-0.2950.3064-0.00220.38070.0438-0.05960.55210.03850.31814.819627.433816.6983
40.02540.00030.02040.0534-0.04460.0453-0.3314-0.1515-0.3645-0.16270.102-0.31090.34431.1997-0.00070.36470.1188-0.00040.6884-0.04510.514520.878416.254410.8104
51.16420.90360.55441.36150.17580.7352-0.4175-0.2466-0.560.17520.5504-0.28560.32960.19470.06420.33260.30840.01060.30870.1840.40356.91710.792124.2822
60.21430.07120.08140.48190.12130.092-0.11930.2473-0.15280.34620.4938-0.44060.13230.78870.09550.52390.3147-0.12110.5447-0.00910.601822.852619.174121.457
70.0704-0.03830.00650.11440.0131-0.01790.4367-0.5750.7280.8232-0.3036-0.0547-0.07730.17440.0010.73210.0197-0.02030.6707-0.01270.555520.920736.922524.7699
80.30260.0227-0.01820.0971-0.17540.19160.0164-0.2327-0.46470.0506-0.0031-0.21570.2579-0.2546-0.00030.55030.06140.02220.37830.03560.482123.0605-12.421133.4221
90.17320.2199-0.08680.1852-0.00510.0581-0.0794-0.5366-0.209-0.0725-0.0901-0.112-0.06130.3995-0.13580.6951-0.00150.07051.08090.05370.467942.57990.175852.0387
100.0957-0.1147-0.02580.11530.00460.08110.301-0.2522-0.36080.3567-0.28590.03140.3940.0520.00010.40630.11270.03090.49980.0730.395639.6859-1.946334.3449
110.41360.2212-0.05290.2223-0.0147-0.00640.08660.1571-0.08210.0202-0.0313-0.11160.0017-0.22590.00020.40920.14110.02910.298-0.00580.390532.0523-2.685222.919
120.0574-0.03430.08090.0423-0.02470.08410.42-0.8506-0.13410.2985-0.44640.1328-0.0610.0437-0.00010.76440.12870.01920.6802-0.0210.520332.57772.348148.2369
130.0320.001-0.01370.02490.04230.0484-0.062-0.07480.0153-0.15530.3103-0.1772-0.50850.1508-0.00051.1167-0.23750.08440.701-0.07180.590339.043215.266143.6867
140.01820.0276-0.01050.01980.00880.02490.2128-0.22850.0898-0.1439-0.25350.1922-0.8431-0.233700.63140.0730.09960.5079-0.00590.520524.32157.599339.8969
150.7109-0.26750.31940.443-0.42480.31240.250.1672-0.1226-0.1091-0.04330.2369-0.286-0.3252-0.00010.34250.1246-0.01190.33660.01920.416819.3246-4.08524.0474
160.00830.00440.06270.0277-0.19610.28410.2791-0.11480.2246-0.04420.05790.1656-0.95580.06840.01110.42380.02070.04210.36650.00970.52927.85619.601629.7703
170.0178-0.01350.0020.00570.00270.0325-0.16640.0963-0.2239-0.2477-0.5372-0.0240.24380.3854-0.00120.87160.12610.04180.5812-0.10360.849651.02045.821831.3848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 206 through 237 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 238 through 276 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 277 through 364 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 365 through 377 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 378 through 430 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 431 through 459 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 460 through 475 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 207 through 238 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 239 through 277 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 278 through 302 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 303 through 333 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 334 through 353 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 354 through 364 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 365 through 377 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 378 through 430 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 431 through 458 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 459 through 475 )B0

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