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- PDB-9iwm: X-ray structure of human PPARalpha ligand binding domain-GW7647-T... -

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Basic information

Entry
Database: PDB / ID: 9iwm
TitleX-ray structure of human PPARalpha ligand binding domain-GW7647-TRAP220 coactivator peptide co-crystals obtained by cross-seeding
Components
  • Mediator of RNA polymerase II transcription subunit 1
  • Peroxisome proliferator-activated receptor alpha
KeywordsTRANSCRIPTION / Nuclear receptor / Protein-ligand complex / PPAR / Coactivator / TRAP220
Function / homology
Function and homology information


positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enucleate erythrocyte development / regulation of RNA biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / androgen biosynthetic process / positive regulation of G0 to G1 transition / enamel mineralization / retinal pigment epithelium development / negative regulation of cell growth involved in cardiac muscle cell development ...positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enucleate erythrocyte development / regulation of RNA biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / androgen biosynthetic process / positive regulation of G0 to G1 transition / enamel mineralization / retinal pigment epithelium development / negative regulation of cell growth involved in cardiac muscle cell development / G0 to G1 transition / mammary gland branching involved in thelarche / thyroid hormone receptor signaling pathway / regulation of ketone metabolic process / cellular response to fructose stimulus / regulation of fatty acid metabolic process / core mediator complex / negative regulation of appetite / regulation of vitamin D receptor signaling pathway / positive regulation of fatty acid beta-oxidation / lipoprotein metabolic process / positive regulation of fatty acid oxidation / behavioral response to nicotine / nuclear retinoic acid receptor binding / ventricular trabecula myocardium morphogenesis / negative regulation of hepatocyte apoptotic process / mediator complex / positive regulation of keratinocyte differentiation / negative regulation of leukocyte cell-cell adhesion / mitogen-activated protein kinase kinase kinase binding / thyroid hormone generation / Generic Transcription Pathway / peroxisome proliferator activated receptor binding / embryonic heart tube development / cellular response to thyroid hormone stimulus / ubiquitin conjugating enzyme binding / negative regulation of glycolytic process / positive regulation of hepatocyte proliferation / nuclear vitamin D receptor binding / embryonic hindlimb morphogenesis / nuclear thyroid hormone receptor binding / lens development in camera-type eye / embryonic hemopoiesis / megakaryocyte development / positive regulation of fatty acid metabolic process / cellular response to hepatocyte growth factor stimulus / DNA-binding transcription activator activity / cellular response to steroid hormone stimulus / nuclear steroid receptor activity / positive regulation of intracellular estrogen receptor signaling pathway / positive regulation of ATP biosynthetic process / histone acetyltransferase binding / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / NFAT protein binding / negative regulation of cholesterol storage / RSV-host interactions / fat cell differentiation / mammary gland branching involved in pregnancy / monocyte differentiation / negative regulation of macrophage derived foam cell differentiation / general transcription initiation factor binding / negative regulation of neuron differentiation / epidermis development / hematopoietic stem cell differentiation / positive regulation of transcription initiation by RNA polymerase II / negative regulation of keratinocyte proliferation / ubiquitin ligase complex / nuclear receptor-mediated steroid hormone signaling pathway / embryonic placenta development / animal organ regeneration / erythrocyte development / phosphatase binding / positive regulation of lipid biosynthetic process / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / intracellular receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / nitric oxide metabolic process / negative regulation of blood pressure / hormone-mediated signaling pathway / : / MDM2/MDM4 family protein binding / lactation / 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 / cellular response to epidermal growth factor stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / positive regulation of erythrocyte differentiation / liver development / cellular response to starvation / nuclear receptor binding / gluconeogenesis
Similarity search - Function
Peroxisome proliferator-activated receptor alpha / : / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / Peroxisome proliferator-activated receptor / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type ...Peroxisome proliferator-activated receptor alpha / : / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / Peroxisome proliferator-activated 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
Similarity search - Domain/homology
Chem-2VN / Peroxisome proliferator-activated receptor alpha / Mediator of RNA polymerase II transcription subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 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

Downloads & links

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Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor alpha
B: Mediator of RNA polymerase II transcription subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6484
Polymers33,0542
Non-polymers5952
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-11 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.012, 61.916, 52.944
Angle α, β, γ (deg.)90.00, 106.61, 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 Mediator of RNA polymerase II transcription subunit 1 / Activator-recruited cofactor 205 kDa component / ARC205 / Mediator complex subunit 1 / Peroxisome ...Activator-recruited cofactor 205 kDa component / ARC205 / Mediator complex subunit 1 / Peroxisome proliferator-activated receptor-binding protein / PBP / PPAR-binding protein / Thyroid hormone receptor-associated protein complex 220 kDa component / Trap220 / Thyroid receptor-interacting protein 2 / TR-interacting protein 2 / TRIP-2 / Vitamin D receptor-interacting protein complex component DRIP205 / p53 regulatory protein RB18A


Mass: 2197.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15648
#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: 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.: 146 / 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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.1M Tris (pH 8.5), 25% PEG 3350, 0.2M Ammonium acetate

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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: Dec 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: 1.39→43.13 Å / Num. obs: 54656 / % possible obs: 97.5 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.022 / Rrim(I) all: 0.042 / Net I/σ(I): 17.1 / Num. measured all: 186839
Reflection shellResolution: 1.39→1.41 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2641 / CC1/2: 0.924 / Rpim(I) all: 0.213 / Rrim(I) all: 0.403 / % possible all: 95.7

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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: 1.39→43.13 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 21.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2048 5099 4.91 %
Rwork0.1835 --
obs0.1845 54640 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.39→43.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 41 146 2376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142318
X-RAY DIFFRACTIONf_angle_d1.3513126
X-RAY DIFFRACTIONf_dihedral_angle_d15.773881
X-RAY DIFFRACTIONf_chiral_restr0.088356
X-RAY DIFFRACTIONf_plane_restr0.009393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.40580.27251430.24743152X-RAY DIFFRACTION87
1.4058-1.42240.25011860.24143136X-RAY DIFFRACTION93
1.4224-1.43970.28391700.22733229X-RAY DIFFRACTION92
1.4397-1.45790.25671420.21883282X-RAY DIFFRACTION93
1.4579-1.47710.24081990.20993246X-RAY DIFFRACTION93
1.4771-1.49740.24431760.20033281X-RAY DIFFRACTION93
1.4974-1.51880.24861970.20313204X-RAY DIFFRACTION94
1.5188-1.54140.22361430.20163238X-RAY DIFFRACTION93
1.5414-1.56550.21731390.20243372X-RAY DIFFRACTION93
1.5655-1.59120.23251730.19093192X-RAY DIFFRACTION93
1.5912-1.61860.21341450.19393255X-RAY DIFFRACTION93
1.6186-1.64810.22811650.18573238X-RAY DIFFRACTION93
1.6481-1.67980.2311410.19083295X-RAY DIFFRACTION93
1.6798-1.7140.22871850.19113247X-RAY DIFFRACTION93
1.714-1.75130.23821620.19073306X-RAY DIFFRACTION95
1.7513-1.79210.22021890.18043302X-RAY DIFFRACTION95
1.7921-1.83690.2321520.18613338X-RAY DIFFRACTION95
1.8369-1.88650.17921710.18213375X-RAY DIFFRACTION95
1.8865-1.9420.24181960.19033268X-RAY DIFFRACTION95
1.942-2.00470.24361590.19683338X-RAY DIFFRACTION95
2.0047-2.07640.20761550.1873355X-RAY DIFFRACTION96
2.0764-2.15950.21372050.18113274X-RAY DIFFRACTION95
2.1595-2.25780.18231810.17843337X-RAY DIFFRACTION95
2.2578-2.37680.19791730.17883299X-RAY DIFFRACTION95
2.3768-2.52570.21871450.19223262X-RAY DIFFRACTION93
2.5257-2.72070.20461790.18873314X-RAY DIFFRACTION95
2.7207-2.99440.18881720.19463342X-RAY DIFFRACTION95
2.9944-3.42760.22371710.19353396X-RAY DIFFRACTION97
3.4276-4.31780.17291830.15763414X-RAY DIFFRACTION99
4.3178-43.130.16942020.15913387X-RAY DIFFRACTION97

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