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- PDB-4jaz: Crystal structure of the complex between PPARgamma LBD and trans-... -

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Basic information

Entry
Database: PDB / ID: 4jaz
TitleCrystal structure of the complex between PPARgamma LBD and trans-resveratrol
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION REGULATION / BUNDLE OF ALPHA-HELICES / SMALL FOUR-STRNDED BETA-SHEET / ACTIVATOR / DIABETES MELLITUS / DISEASE MUTATION / DNA-BINDING / NUCLEUS / OBESITY / PHOSPHORYLATION / RECEPTOR / TRANSCRIPTION
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 / positive regulation of fatty acid metabolic process / STAT family protein binding / response to lipid / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / negative regulation of SMAD protein signal transduction / E-box binding / lipid homeostasis / alpha-actinin binding / R-SMAD binding / negative regulation of vascular associated smooth muscle cell proliferation / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / white fat cell 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 BMP signaling pathway / positive regulation of cholesterol efflux / cell fate commitment / negative regulation of osteoblast differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / 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 / negative regulation of MAPK cascade / intracellular receptor signaling pathway / hormone-mediated signaling pathway / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / response to nutrient / epithelial cell differentiation / regulation of cellular response to insulin stimulus / peptide binding / negative regulation of miRNA transcription / negative regulation of angiogenesis / placenta development / positive regulation of apoptotic signaling pathway / Regulation of PTEN gene transcription / transcription coregulator binding / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / mRNA transcription by RNA polymerase II / fatty acid metabolic process / negative regulation of transforming growth factor beta receptor signaling pathway / PPARA activates gene expression / regulation of circadian rhythm / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / lipid metabolic process / positive regulation of miRNA transcription / regulation of blood pressure / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / nuclear receptor activity / cellular response to insulin stimulus / rhythmic process / glucose homeostasis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to hypoxia / DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / receptor complex / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / innate immune response / 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
RESVERATROL / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.85 Å
AuthorsPochetti, G. / Capelli, D. / Montanari, R. / Calleri, E. / Moaddel, R. / Temporini, C.
CitationJournal: Chembiochem / Year: 2014
Title: Resveratrol and Its Metabolites Bind to PPARs.
Authors: Calleri, E. / Pochetti, G. / Dossou, K.S. / Laghezza, A. / Montanari, R. / Capelli, D. / Prada, E. / Loiodice, F. / Massolini, G. / Bernier, M. / Moaddel, R.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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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)65,6163
Polymers65,3882
Non-polymers2281
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.720, 63.380, 119.760
Angle α, β, γ (deg.)90.00, 102.90, 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: 32693.824 Da / Num. of mol.: 2 / Fragment: UNP residues 223-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P37231
#2: Chemical ChemComp-STL / RESVERATROL


Mass: 228.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.8M NA CITRATE, 0.15M TRIS, PH8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 21, 2012
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR (SI 111 AND SI 220)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 13805 / Num. obs: 13805 / % possible obs: 86.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 7.2
Reflection shellResolution: 2.85→3 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2012 / % possible all: 86.3

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementResolution: 2.85→10 Å / Occupancy max: 1 / Occupancy min: 0 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2635 675 4.3 %
Rwork0.2368 12751 -
obs-13426 85 %
Solvent computationBsol: 86.5172 Å2
Displacement parametersBiso max: 150 Å2 / Biso mean: 64.5481 Å2 / Biso min: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1--5.849 Å20 Å25.276 Å2
2--15.614 Å20 Å2
3----9.764 Å2
Refinement stepCycle: LAST / Resolution: 2.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4289 0 17 132 4438
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_d1.569
X-RAY DIFFRACTIONc_mcbond_it2.7062
X-RAY DIFFRACTIONc_scbond_it3.5762.5
X-RAY DIFFRACTIONc_mcangle_it4.4682.5
X-RAY DIFFRACTIONc_scangle_it5.3143

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