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- PDB-3sp6: Structural basis for iloprost as a dual PPARalpha/delta agonist -

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Basic information

Entry
Database: PDB / ID: 3sp6
TitleStructural basis for iloprost as a dual PPARalpha/delta agonist
Components
  • Peroxisome proliferator-activated receptor alpha
  • Peroxisome proliferator-activated receptor gamma coactivator 1-beta
KeywordsTRANSCRIPTION / PPAR LBD / nuclear receptor fold / ligand binding / gene transcription
Function / homology
Function and homology information


AF-2 domain binding / positive regulation of transformation of host cell by virus / regulation of fatty acid transport / bone trabecula formation / regulation of fatty acid metabolic process / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of fatty acid oxidation / regulation of cellular ketone metabolic process / cellular response to fructose stimulus ...AF-2 domain binding / positive regulation of transformation of host cell by virus / regulation of fatty acid transport / bone trabecula formation / regulation of fatty acid metabolic process / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of fatty acid oxidation / regulation of cellular ketone metabolic process / cellular response to fructose stimulus / behavioral response to nicotine / negative regulation of appetite / mitochondrial transcription / positive regulation of fatty acid beta-oxidation / lipoprotein metabolic process / mediator complex / negative regulation of hepatocyte apoptotic process / mitogen-activated protein kinase kinase kinase binding / negative regulation of leukocyte cell-cell adhesion / positive regulation of osteoclast differentiation / ubiquitin conjugating enzyme binding / negative regulation of glycolytic process / negative regulation of sequestering of triglyceride / nuclear steroid receptor activity / DNA-binding transcription activator activity / positive regulation of fatty acid metabolic process / nitric oxide metabolic process / NFAT protein binding / positive regulation of ATP biosynthetic process / negative regulation of cholesterol storage / negative regulation of macrophage derived foam cell differentiation / negative regulation of cytokine production involved in inflammatory response / epidermis development / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / phosphatase binding / positive regulation of bone resorption / intracellular estrogen receptor signaling pathway / positive regulation of lipid biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of signaling receptor activity / positive regulation of phosphorylation / positive regulation of gluconeogenesis / MDM2/MDM4 family protein binding / RORA activates gene expression / negative regulation of blood pressure / cellular response to starvation / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / ossification / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / negative regulation of miRNA transcription / fatty acid metabolic process / gluconeogenesis / actin filament organization / nuclear estrogen receptor binding / transcription coregulator activity / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / Heme signaling / wound healing / SUMOylation of intracellular receptors / response to insulin / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / Cytoprotection by HMOX1 / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to reactive oxygen species / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Regulation of RUNX2 expression and activity / nuclear receptor activity / Circadian Clock / positive regulation of cold-induced thermogenesis / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of DNA-templated transcription / lipid binding / chromatin / protein-containing complex binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion
Similarity search - Function
PPARGC1B, RNA recognition motif / PGC-1 / Peroxisome proliferator-activated receptor alpha / 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 ...PPARGC1B, RNA recognition motif / PGC-1 / Peroxisome proliferator-activated receptor alpha / 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 / 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 / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-IL2 / Peroxisome proliferator-activated receptor alpha / Peroxisome proliferator-activated receptor gamma coactivator 1-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsRong, H. / Li, Y.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural basis for iloprost as a dual peroxisome proliferator-activated receptor alpha/delta agonist.
Authors: Jin, L. / Lin, S. / Rong, H. / Zheng, S. / Jin, S. / Wang, R. / Li, Y.
History
DepositionJul 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Apr 16, 2014Group: Other
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_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 alpha
B: Peroxisome proliferator-activated receptor gamma coactivator 1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9173
Polymers33,5562
Non-polymers3601
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-9 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.837, 60.973, 54.160
Angle α, β, γ (deg.)90.00, 108.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 32342.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARA, NR1C1, PPAR / Production host: Escherichia coli (E. coli) / References: UniProt: Q07869
#2: Protein/peptide Peroxisome proliferator-activated receptor gamma coactivator 1-beta / PGC-1-beta / PPAR-gamma coactivator 1-beta / PPARGC-1-beta / PGC-1-related estrogen receptor alpha coactivator


Mass: 1213.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q86YN6
#3: Chemical ChemComp-IL2 / (5E)-5-[(3aS,4R,5R,6aS)-5-hydroxy-4-[(1E,3S,4R)-3-hydroxy-4-methyloct-1-en-6-yn-1-yl]hexahydropentalen-2(1H)-ylidene]pentanoic acid


Mass: 360.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H32O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 15, 2010
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 13835 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.21-2.38199
2.38-2.62199
2.62-31100
3-3.781100
3.78-501100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→28.428 Å / SU ML: 0.2 / σ(F): 1.38 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 690 4.99 %RANDOM
Rwork0.1764 ---
obs0.1794 13835 99.38 %-
all-13835 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.178 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6492 Å20 Å20.2828 Å2
2--0.3898 Å2-0 Å2
3---0.2594 Å2
Refinement stepCycle: LAST / Resolution: 2.21→28.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 26 88 2335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082284
X-RAY DIFFRACTIONf_angle_d1.133078
X-RAY DIFFRACTIONf_dihedral_angle_d17.323859
X-RAY DIFFRACTIONf_chiral_restr0.068363
X-RAY DIFFRACTIONf_plane_restr0.004388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.38150.22141420.16212537X-RAY DIFFRACTION97
2.3815-2.6210.24861430.1712636X-RAY DIFFRACTION100
2.621-2.99990.25641370.17472629X-RAY DIFFRACTION100
2.9999-3.77810.2411360.17252637X-RAY DIFFRACTION100
3.7781-28.43070.23141320.18182706X-RAY DIFFRACTION100

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