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- PDB-3t03: Crystal structure of PPAR gamma ligand binding domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 3t03
TitleCrystal structure of PPAR gamma ligand binding domain in complex with a novel partial agonist GQ-16
Components
  • Nuclear receptor coactivator 1
  • Peroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION/TRANSCRIPTION REGULATOR / Protein-Drug Complex / THIAZOLIDINEDIONES / Ligand Binding Protein / Transcription factor / Nucleus Receptor / TRANSCRIPTION-TRANSCRIPTION REGULATOR complex
Function / homology
Function and homology information


labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / 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 / positive regulation of transcription from RNA polymerase II promoter by galactose / MECP2 regulates transcription factors / positive regulation of female receptivity / negative regulation of extracellular matrix assembly ...labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / 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 / positive regulation of transcription from RNA polymerase II promoter by galactose / MECP2 regulates transcription factors / positive regulation of female receptivity / 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 / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / DNA binding domain binding / STAT family protein binding / hypothalamus development / positive regulation of fatty acid metabolic process / male mating behavior / response to lipid / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / 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 / cellular response to low-density lipoprotein particle stimulus / negative regulation of lipid storage / negative regulation of blood vessel endothelial cell migration / negative regulation of BMP signaling pathway / cellular response to Thyroglobulin triiodothyronine / white fat cell differentiation / negative regulation of mitochondrial fission / estrous cycle / Synthesis of bile acids and bile salts / 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 / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / BMP signaling pathway / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / long-chain fatty acid transport / nuclear retinoid X receptor binding / response to retinoic acid / histone acetyltransferase activity / negative regulation of signaling receptor activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cell maturation / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / negative regulation of angiogenesis / cerebellum development / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / negative regulation of miRNA transcription / negative regulation of MAP kinase activity / fatty acid metabolic process / Regulation of PTEN gene transcription / response to progesterone / transcription coregulator binding / nuclear estrogen receptor binding / hippocampus development / nuclear receptor binding / placenta development / negative regulation of smooth muscle cell proliferation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II
Similarity search - Function
Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator ...Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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-3T0 / Peroxisome proliferator-activated receptor gamma / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRajagopalan, S. / Webb, P. / Baxter, J.D. / Brennan, R.G. / Phillips, K.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: GQ-16, a novel peroxisome proliferator-activated receptor (PPAR gamma) ligand, promotes insulin sensitization without weight gain.
Authors: Amato, A.A. / Rajagopalan, S. / Lin, J.Z. / Carvalho, B.M. / Figueira, A.C. / Lu, J. / Ayers, S.D. / Mottin, M. / Silveira, R.L. / Souza, P.C. / Mourao, R.H. / Saad, M.J. / Togashi, M. / ...Authors: Amato, A.A. / Rajagopalan, S. / Lin, J.Z. / Carvalho, B.M. / Figueira, A.C. / Lu, J. / Ayers, S.D. / Mottin, M. / Silveira, R.L. / Souza, P.C. / Mourao, R.H. / Saad, M.J. / Togashi, M. / Simeoni, L.A. / Abdalla, D.S. / Skaf, M.S. / Polikparpov, I. / Lima, M.C. / Galdino, S.L. / Brennan, R.G. / Baxter, J.D. / Pitta, I.R. / Webb, P. / Phillips, K.J. / Neves, F.A.
History
DepositionJul 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 13, 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
C: Nuclear receptor coactivator 1
D: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8756
Polymers69,0384
Non-polymers8372
Water5,693316
1
A: Peroxisome proliferator-activated receptor gamma
C: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9373
Polymers34,5192
Non-polymers4181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peroxisome proliferator-activated receptor gamma
D: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9373
Polymers34,5192
Non-polymers4181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.690, 84.390, 96.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 32399.512 Da / Num. of mol.: 2 / Fragment: UNP residues 234-505 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P37231
#2: Protein/peptide Nuclear receptor coactivator 1 / / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal ...NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal carcinoma antigen NY-REN-52 / Steroid receptor coactivator 1 / SRC-1


Mass: 2119.448 Da / Num. of mol.: 2 / Fragment: UNP residues 683-700 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-3T0 / (5Z)-5-(5-bromo-2-methoxybenzylidene)-3-(4-methylbenzyl)-1,3-thiazolidine-2,4-dione


Mass: 418.304 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16BrNO3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate, pH 5.6, 30%(w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 25, 2009
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→42.54 Å / Num. obs: 67318 / % possible obs: 98 %

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: dev_788)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FUR

3fur


Resolution: 2.1→42.044 Å / SU ML: 0.57 / σ(F): 1.34 / Phase error: 26.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 4017 10.06 %RANDOM
Rwork0.2084 ---
obs0.2122 39920 97.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.696 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.9077 Å20 Å2-0 Å2
2--20.2744 Å20 Å2
3----7.9998 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4249 0 50 316 4615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014374
X-RAY DIFFRACTIONf_angle_d1.3175900
X-RAY DIFFRACTIONf_dihedral_angle_d15.7251644
X-RAY DIFFRACTIONf_chiral_restr0.074682
X-RAY DIFFRACTIONf_plane_restr0.005741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17510.32243990.29773478X-RAY DIFFRACTION97
2.1751-2.26220.32244290.29153461X-RAY DIFFRACTION97
2.2622-2.36510.29853780.26133561X-RAY DIFFRACTION98
2.3651-2.48980.28274130.22933549X-RAY DIFFRACTION98
2.4898-2.64580.2683830.22823609X-RAY DIFFRACTION98
2.6458-2.850.24984160.2213577X-RAY DIFFRACTION99
2.85-3.13670.29064050.23253603X-RAY DIFFRACTION98
3.1367-3.59040.24224010.21233629X-RAY DIFFRACTION99
3.5904-4.52270.21743820.16383659X-RAY DIFFRACTION98
4.5227-42.05210.21314110.19263777X-RAY DIFFRACTION97

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