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- PDB-9iwn: X-ray structure of human PPARalpha ligand binding domain-intrinsi... -

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Basic information

Entry
Database: PDB / ID: 9iwn
TitleX-ray structure of human PPARalpha ligand binding domain-intrinsic fatty acid (E. coli origin)-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 / regulation of ketone metabolic process / cellular response to fructose stimulus / 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 / regulation of ketone metabolic process / cellular response to fructose stimulus / 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 / lncRNA binding / response to muscle activity / 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 / negative regulation of cytokine production involved in inflammatory response / response to nutrient / 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 / respiratory electron transport chain / gluconeogenesis / fatty acid metabolic process / mitochondrion organization / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / response to insulin / 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 / cellular response to oxidative stress / protein-containing complex assembly / 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
PALMITIC ACID / 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: 1.59 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)32,8584
Polymers32,5092
Non-polymers3492
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-10 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.027, 61.496, 53.274
Angle α, β, γ (deg.)90.00, 106.29, 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-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.18 Å3/Da / Density % sol: 43.52 %
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: 1.59→43.22 Å / Num. obs: 37488 / % possible obs: 99.8 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.033 / Rrim(I) all: 0.061 / Net I/σ(I): 14 / Num. measured all: 128017
Reflection shellResolution: 1.59→1.62 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1857 / CC1/2: 0.874 / Rpim(I) all: 0.224 / Rrim(I) all: 0.424 / % possible all: 99.2

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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: 1.59→43.219 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 20.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2081 3522 4.94 %
Rwork0.186 --
obs0.1871 37468 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→43.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 0 24 109 2292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012272
X-RAY DIFFRACTIONf_angle_d1.023061
X-RAY DIFFRACTIONf_dihedral_angle_d11.51407
X-RAY DIFFRACTIONf_chiral_restr0.057352
X-RAY DIFFRACTIONf_plane_restr0.006388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5904-1.61220.28851350.23242683X-RAY DIFFRACTION94
1.6122-1.63520.22841330.22032642X-RAY DIFFRACTION98
1.6352-1.65960.22531610.20752783X-RAY DIFFRACTION98
1.6596-1.68560.25641150.21352707X-RAY DIFFRACTION97
1.6856-1.71320.2211420.2062788X-RAY DIFFRACTION98
1.7132-1.74270.23931650.20452710X-RAY DIFFRACTION97
1.7427-1.77440.24251290.19942701X-RAY DIFFRACTION97
1.7744-1.80860.23631380.19692771X-RAY DIFFRACTION97
1.8086-1.84550.2091190.19132729X-RAY DIFFRACTION97
1.8455-1.88560.20631640.19042667X-RAY DIFFRACTION97
1.8856-1.92950.25651430.19082691X-RAY DIFFRACTION97
1.9295-1.97770.23021460.19492764X-RAY DIFFRACTION97
1.9777-2.03120.25991320.20692633X-RAY DIFFRACTION95
2.0312-2.0910.1941610.19262604X-RAY DIFFRACTION94
2.091-2.15850.21591550.18072692X-RAY DIFFRACTION97
2.1585-2.23560.20051250.18092732X-RAY DIFFRACTION97
2.2356-2.32510.19051680.17962738X-RAY DIFFRACTION98
2.3251-2.43090.22031370.17782731X-RAY DIFFRACTION98
2.4309-2.55910.22731300.18982749X-RAY DIFFRACTION98
2.5591-2.71940.20291370.1992707X-RAY DIFFRACTION97
2.7194-2.92930.22111270.20192735X-RAY DIFFRACTION96
2.9293-3.2240.2181350.20292688X-RAY DIFFRACTION96
3.224-3.69030.21061290.1812651X-RAY DIFFRACTION94
3.6903-4.64850.15771460.152677X-RAY DIFFRACTION97
4.6485-43.2190.18331500.16612806X-RAY DIFFRACTION99

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