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- PDB-2fvj: A novel anti-adipogenic partial agonist of peroxisome proliferato... -

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Basic information

Entry
Database: PDB / ID: 2fvj
TitleA novel anti-adipogenic partial agonist of peroxisome proliferator-activated receptor-gamma (PPARG) recruits pparg-coactivator-1 alpha (PGC1A) but potentiates insulin signaling in vitro
Components
  • Nuclear receptor coactivator 1
  • Peroxisome proliferator-activated receptor gamma
KeywordsSIGNALING PROTEIN / Nuclear Receptor LBD / Alpha Helical Sandwich
Function / homology
Function and homology information


labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / 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 female receptivity / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly ...labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / 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 female receptivity / 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 / hypothalamus development / male mating behavior / STAT family protein binding / positive regulation of fatty acid metabolic process / 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 / negative regulation of blood vessel endothelial cell migration / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / estrous cycle / 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 / cellular response to Thyroglobulin triiodothyronine / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / Synthesis of bile acids and bile salts / 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 / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / negative regulation of signaling receptor activity / histone acetyltransferase activity / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / cell maturation / histone acetyltransferase / cellular response to hormone stimulus / positive regulation of adipose tissue development / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / RORA activates gene expression / lactation / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / cerebellum development / negative regulation of angiogenesis / response to nutrient / negative regulation of MAP kinase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / fatty acid metabolic process / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / response to progesterone / placenta development / Regulation of PTEN gene transcription / negative regulation of smooth muscle cell proliferation / nuclear estrogen receptor binding / transcription coregulator binding / nuclear receptor binding / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / SUMOylation of intracellular receptors / Heme signaling / 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-RO0 / Peroxisome proliferator-activated receptor gamma / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.99 Å
AuthorsBenz, J. / Burgermeister, E. / Flament, A. / Schnoebelen, A. / Stihle, M. / Gsell, B. / Rufer, A. / Ruf, A. / Kuhn, B. / Maerki, H.P. ...Benz, J. / Burgermeister, E. / Flament, A. / Schnoebelen, A. / Stihle, M. / Gsell, B. / Rufer, A. / Ruf, A. / Kuhn, B. / Maerki, H.P. / Mizrahi, J. / Sebokova, E. / Niesor, E. / Meyer, M.
CitationJournal: Mol.Endocrinol. / Year: 2006
Title: A novel partial agonist of peroxisome proliferator-activated receptor-gamma (PPARgamma) recruits PPARgamma-coactivator-1alpha, prevents triglyceride accumulation, and potentiates insulin signaling in vitro
Authors: Burgermeister, E. / Schnoebelen, A. / Flament, A. / Benz, J. / Stihle, M. / Gsell, B. / Rufer, A. / Ruf, A. / Kuhn, B. / Maerki, H.P. / Mizrahi, J. / Sebokova, E. / Niesor, E. / Meyer, M.
History
DepositionJan 31, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor gamma
B: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1034
Polymers32,4692
Non-polymers6352
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-19 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.483, 65.897, 87.538
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


Mass: 30997.021 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 207-477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P37231
#2: Protein/peptide Nuclear receptor coactivator 1 / / NCoA-1 / Steroid receptor coactivator-1 / SRC-1 / RIP160 / Hin-2 protein


Mass: 1471.697 Da / Num. of mol.: 1
Fragment: COACTIVATOR FRAGMENT SRC-1, 13-mer peptide from Nuclear receptor coactivator 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-RO0 / 1-(3,4-DIMETHOXYBENZYL)-6,7-DIMETHOXY-4-{[4-(2-METHOXYPHENYL)PIPERIDIN-1-YL]METHYL}ISOQUINOLINE / ISOQUINOLINE DERIVATIVE PA-082


Mass: 542.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H38N2O5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG3350, 0.2M magnesium chloride, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.7997 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 30, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7997 Å / Relative weight: 1
ReflectionResolution: 1.99→30 Å / Num. all: 21716 / Num. obs: 21716 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.07 Å / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: IN HOUSE PPARG STRUCTURE

Resolution: 1.99→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.752 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24586 1105 5.1 %RANDOM
Rwork0.18942 ---
all0.19225 21575 --
obs0.19225 21575 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.317 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--1.84 Å20 Å2
3----1.73 Å2
Refinement stepCycle: LAST / Resolution: 1.99→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2149 0 46 253 2448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222232
X-RAY DIFFRACTIONr_angle_refined_deg1.5822.0153008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4445265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5925.36895
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51115427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.156158
X-RAY DIFFRACTIONr_chiral_restr0.1250.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021619
X-RAY DIFFRACTIONr_nbd_refined0.2210.21091
X-RAY DIFFRACTIONr_nbtor_refined0.310.21540
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2207
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.290.228
X-RAY DIFFRACTIONr_mcbond_it1.0961.51382
X-RAY DIFFRACTIONr_mcangle_it1.7822166
X-RAY DIFFRACTIONr_scbond_it2.70931010
X-RAY DIFFRACTIONr_scangle_it4.184.5842
LS refinement shellResolution: 1.994→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 68 -
Rwork0.201 1405 -
obs--95.03 %

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