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- PDB-9iwo: X-ray structure of human PPARalpha ligand binding domain-GW7647-P... -

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Basic information

Entry
Database: PDB / ID: 9iwo
TitleX-ray structure of human PPARalpha ligand binding domain-GW7647-PGC1alpha coactivator peptide co-crystals obtained by cross-seeding
Components
  • Peroxisome proliferator-activated receptor alpha
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
KeywordsTRANSCRIPTION / Nuclear receptor / Protein-ligand complex / PPAR / Coactivator / PGC1a
Function / homology
Function and homology information


Regulation of MITF-M dependent genes involved in metabolism / positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / cellular response to fructose stimulus / regulation of ketone metabolic process / regulation of fatty acid metabolic process / negative regulation of appetite / positive regulation of fatty acid beta-oxidation ...Regulation of MITF-M dependent genes involved in metabolism / positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / cellular response to fructose stimulus / regulation of ketone metabolic process / regulation of fatty acid metabolic process / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / lipoprotein metabolic process / positive regulation of fatty acid oxidation / behavioral response to nicotine / cellular respiration / negative regulation of hepatocyte apoptotic process / negative regulation of leukocyte cell-cell adhesion / mitogen-activated protein kinase kinase kinase binding / ubiquitin conjugating enzyme binding / negative regulation of glycolytic process / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / positive regulation of fatty acid metabolic process / DNA-binding transcription activator activity / nuclear steroid receptor activity / temperature homeostasis / positive regulation of ATP biosynthetic process / response to muscle activity / lncRNA binding / NFAT protein binding / negative regulation of cholesterol storage / response to starvation / intracellular glucose homeostasis / fatty acid oxidation / response to dietary excess / negative regulation of macrophage derived foam cell differentiation / epidermis development / adipose tissue development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / phosphatase binding / brown fat cell differentiation / positive regulation of lipid biosynthetic process / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / energy homeostasis / intracellular receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / digestion / nitric oxide metabolic process / negative regulation of blood pressure / hormone-mediated signaling pathway / : / MDM2/MDM4 family protein binding / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / response to nutrient / negative regulation of cytokine production involved in inflammatory response / positive regulation of gluconeogenesis / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / RNA splicing / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / positive regulation of DNA-binding transcription factor activity / cellular response to starvation / nuclear receptor binding / gluconeogenesis / fatty acid metabolic process / respiratory electron transport chain / mitochondrion organization / transcription coregulator activity / response to insulin / transcription initiation at RNA polymerase II promoter / 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 / wound healing / Heme signaling / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / PPARA activates gene expression / regulation of circadian rhythm / Cytoprotection by HMOX1 / PML body / Nuclear Receptor transcription pathway / chromatin DNA binding / Transcriptional regulation of white adipocyte differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / nuclear receptor activity / mRNA processing / Regulation of RUNX2 expression and activity / : / positive regulation of cold-induced thermogenesis / heart development / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / cellular response to oxidative stress / neuron apoptotic process / gene expression
Similarity search - Function
PGC-1alpha, RNA recognition motif / PGC-1 / Peroxisome proliferator-activated receptor alpha / Peroxisome proliferator-activated receptor / : / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily ...PGC-1alpha, RNA recognition motif / PGC-1 / Peroxisome proliferator-activated receptor alpha / Peroxisome proliferator-activated 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
Similarity search - Domain/homology
Chem-2VN / Peroxisome proliferator-activated receptor alpha / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsKamata, S. / Honda, A. / Yashiro, S. / Komori, Y. / Shimamura, A. / Hosoda, A. / Oyama, T. / Ishii, I.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22K15049 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101071 Japan
CitationJournal: Antioxidants / Year: 2025
Title: Competitive Ligand-Induced Recruitment of Coactivators to Specific PPAR alpha / delta / gamma Ligand-Binding Domains Revealed by Dual-Emission FRET and X-Ray Diffraction of Cocrystals.
Authors: Kamata, S. / Honda, A. / Yashiro, S. / Kaneko, C. / Komori, Y. / Shimamura, A. / Masuda, R. / Oyama, T. / Ishii, I.
History
DepositionJul 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,0123
Polymers32,5092
Non-polymers5031
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-9 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.022, 62.201, 53.312
Angle α, β, γ (deg.)90.00, 106.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peroxisome proliferator-activated receptor alpha


Mass: 30856.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q07869
#2: Protein/peptide Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / PGC-1-alpha / PPAR-gamma coactivator 1-alpha / PPARGC-1-alpha / Ligand effect modulator 6


Mass: 1652.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2
#3: Chemical ChemComp-2VN / 2-[(4-{2-[(4-cyclohexylbutyl)(cyclohexylcarbamoyl)amino]ethyl}phenyl)sulfanyl]-2-methylpropanoic acid


Mass: 502.752 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H46N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.1M HEPES (pH 7.0), 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 23, 2023 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→43.24 Å / Num. obs: 46042 / % possible obs: 99.7 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.021 / Rrim(I) all: 0.04 / Net I/σ(I): 17.6 / Num. measured all: 154864
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 3 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 3 / Num. unique obs: 2254 / CC1/2: 0.892 / Rpim(I) all: 0.233 / Rrim(I) all: 0.416 / % possible all: 99.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX(1.11.1_2575-000)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→43.24 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 23.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2135 4254 4.86 %
Rwork0.1938 --
obs0.1948 46018 96.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→43.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2154 0 35 101 2290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112266
X-RAY DIFFRACTIONf_angle_d1.0813058
X-RAY DIFFRACTIONf_dihedral_angle_d14.71857
X-RAY DIFFRACTIONf_chiral_restr0.075352
X-RAY DIFFRACTIONf_plane_restr0.006383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.5070.34341090.26072625X-RAY DIFFRACTION90
1.507-1.52470.25631480.2632673X-RAY DIFFRACTION94
1.5247-1.54330.30931580.24782753X-RAY DIFFRACTION96
1.5433-1.56280.28041420.24392819X-RAY DIFFRACTION97
1.5628-1.58340.2841510.24132692X-RAY DIFFRACTION96
1.5834-1.60510.2571280.22882867X-RAY DIFFRACTION97
1.6051-1.6280.22491220.22812769X-RAY DIFFRACTION98
1.628-1.65230.2881390.21572893X-RAY DIFFRACTION98
1.6523-1.67810.22211400.22022761X-RAY DIFFRACTION98
1.6781-1.70570.25871610.22022808X-RAY DIFFRACTION98
1.7057-1.73510.29821500.22012801X-RAY DIFFRACTION97
1.7351-1.76660.26231660.22172752X-RAY DIFFRACTION97
1.7666-1.80060.26381710.21042792X-RAY DIFFRACTION97
1.8006-1.83740.22331370.21072808X-RAY DIFFRACTION97
1.8374-1.87730.22531390.20472758X-RAY DIFFRACTION96
1.8773-1.9210.23571450.20762804X-RAY DIFFRACTION97
1.921-1.9690.256960.20832768X-RAY DIFFRACTION95
1.969-2.02220.26721250.21642731X-RAY DIFFRACTION95
2.0222-2.08180.23951400.20562700X-RAY DIFFRACTION94
2.0818-2.14890.21481480.2062772X-RAY DIFFRACTION96
2.1489-2.22570.21251480.19512755X-RAY DIFFRACTION96
2.2257-2.31490.25511380.19832818X-RAY DIFFRACTION98
2.3149-2.42020.20681360.18642828X-RAY DIFFRACTION98
2.4202-2.54780.21591420.20512830X-RAY DIFFRACTION98
2.5478-2.70740.22311610.19632806X-RAY DIFFRACTION98
2.7074-2.91640.24441480.1992750X-RAY DIFFRACTION96
2.9164-3.20980.211450.2082757X-RAY DIFFRACTION95
3.2098-3.6740.16411270.19012675X-RAY DIFFRACTION93
3.674-4.62810.17841690.15522748X-RAY DIFFRACTION96
4.6281-43.240.15551250.15612883X-RAY DIFFRACTION99

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