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- PDB-3u9q: Ligand binding domain of PPARgamma complexed with Decanoic Acid a... -

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Basic information

Entry
Database: PDB / ID: 3u9q
TitleLigand binding domain of PPARgamma complexed with Decanoic Acid and PGC-1a peptide
Components
  • PGC-1a peptide
  • Peroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / Nuclear receptor / Adipogenesis / RXRa / Nucleus
Function / homology
Function and homology information


Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / cellular respiration / 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 / Activation of PPARGC1A (PGC-1alpha) by phosphorylation ...Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / cellular respiration / 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 / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / 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 / temperature homeostasis / lncRNA binding / response to muscle activity / negative regulation of SMAD protein signal transduction / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / response to starvation / lipid homeostasis / E-box binding / intracellular glucose homeostasis / alpha-actinin binding / negative regulation of vascular associated smooth muscle cell proliferation / fatty acid oxidation / R-SMAD binding / response to dietary excess / 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 / adipose tissue development / BMP signaling pathway / long-chain fatty acid transport / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / nuclear retinoid X receptor binding / brown fat cell differentiation / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cell maturation / energy homeostasis / intracellular receptor signaling pathway / digestion / 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 / positive regulation of gluconeogenesis / negative regulation of miRNA transcription / peptide binding / RNA splicing / SUMOylation of transcription cofactors / negative regulation of angiogenesis / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / positive regulation of apoptotic signaling pathway / Regulation of PTEN gene transcription / nuclear receptor binding / respiratory electron transport chain / gluconeogenesis / fatty acid metabolic process / mitochondrion organization / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / placenta development / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / regulation of circadian rhythm / PML body / Nuclear Receptor transcription pathway / chromatin DNA binding
Similarity search - Function
PGC-1alpha, RNA recognition motif / PGC-1 / 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 / RNA recognition motif ...PGC-1alpha, RNA recognition motif / PGC-1 / 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 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / 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 / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DECANOIC ACID / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.522 Å
AuthorsMalapaka, V.R. / Xu, H.E.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Identification and Mechanism of 10-Carbon Fatty Acid as Modulating Ligand of Peroxisome Proliferator-activated Receptors.
Authors: Malapaka, R.R. / Khoo, S. / Zhang, J. / Choi, J.H. / Zhou, X.E. / Xu, Y. / Gong, Y. / Li, J. / Yong, E.L. / Chalmers, M.J. / Chang, L. / Resau, J.H. / Griffin, P.R. / Chen, Y.E. / Xu, H.E.
History
DepositionOct 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 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

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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: PGC-1a peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8773
Polymers31,7052
Non-polymers1721
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-1 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.726, 54.346, 66.809
Angle α, β, γ (deg.)90.000, 107.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 30704.734 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain, UNP residues 236-504
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1C3, PPARG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37231
#2: Protein/peptide PGC-1a peptide


Mass: 1000.319 Da / Num. of mol.: 1 / Fragment: Peptide, UNP residues 142-150 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2
#3: Chemical ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.2
Details: 0.2 M sodium acetate (pH 6.2), 20% PEG 3350, 15% glycerol and 1 mM concentration of the ligand., VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.62 - 1.91
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2009
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.621
21.911
ReflectionResolution: 1.52→33.082 Å / Num. all: 45773 / Num. obs: 43465 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.522→1.562 Å / % possible all: 97.64

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.522→30.082 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.505 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 2308 5 %RANDOM
Rwork0.1831 ---
all0.221 45773 --
obs0.1851 43465 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 100 Å2 / Biso mean: 20.037 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å2-0.2 Å2
2---0.27 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.522→30.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2123 0 12 394 2529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222166
X-RAY DIFFRACTIONr_angle_refined_deg1.6542.0022911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0895263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24425.38591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17315428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.723158
X-RAY DIFFRACTIONr_chiral_restr0.1130.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211544
X-RAY DIFFRACTIONr_mcbond_it1.0781.51325
X-RAY DIFFRACTIONr_mcangle_it2.0322142
X-RAY DIFFRACTIONr_scbond_it3.1813841
X-RAY DIFFRACTIONr_scangle_it5.2654.5769
LS refinement shellResolution: 1.522→1.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 164 -
Rwork0.221 3150 -
all-3314 -
obs--97.64 %
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)
10.0889-0.0163-0.03910.0609-0.00820.07530.0025-0.0084-0.0020.0071-0.0032-0.00090.00480.00220.00070.0028-0.0013-0.00070.00130.00040.00038.7733-1.61812.4761
21.32870.6529-0.72141.43040.05412.38160.0692-0.02530.06190.0514-0.0296-0.0165-0.10540.0116-0.03960.0069-0.00180.0020.0008-0.00040.004915.133617.562715.5256
36.2083-3.74194.29652.2562-2.592.977-0.1947-0.5803-0.66390.21670.50990.4046-0.2669-0.3905-0.31520.2118-0.01580.12220.15320.06080.11312.14430.423822.8301
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A208 - 476
2X-RAY DIFFRACTION2B142 - 150
3X-RAY DIFFRACTION3A1

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