[English] 日本語
Yorodumi
- PDB-9iwn: X-ray structure of human PPARalpha ligand binding domain-intrinsi... -

+
Open data


ID or keywords:

Loading...

-
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 / positive regulation of fatty acid beta-oxidation / cellular response to fructose stimulus / regulation of ketone metabolic process / regulation of fatty acid metabolic process / negative regulation of cell growth involved in cardiac muscle cell development / negative regulation of appetite ...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 / positive regulation of fatty acid beta-oxidation / cellular response to fructose stimulus / regulation of ketone metabolic process / regulation of fatty acid metabolic process / negative regulation of cell growth involved in cardiac muscle cell development / negative regulation of appetite / negative regulation of hepatocyte apoptotic process / lipoprotein metabolic process / positive regulation of fatty acid oxidation / behavioral response to nicotine / cellular respiration / negative regulation of leukocyte cell-cell adhesion / negative regulation of glycolytic process / ubiquitin conjugating enzyme binding / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / mitogen-activated protein kinase kinase kinase binding / positive regulation of fatty acid metabolic process / temperature homeostasis / response to starvation / DNA-binding transcription activator activity / NFAT protein binding / lncRNA binding / negative regulation of cholesterol storage / response to muscle activity / intracellular glucose homeostasis / response to dietary excess / fatty acid oxidation / positive regulation of ATP biosynthetic process / energy homeostasis / nuclear steroid receptor activity / 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 / intracellular receptor signaling pathway / negative regulation of blood pressure / digestion / nitric oxide metabolic process / hormone-mediated signaling pathway / negative regulation of reactive oxygen species biosynthetic process / : / Regulation of lipid metabolism by PPARalpha / response to nutrient / peroxisome proliferator activated receptor signaling pathway / MDM2/MDM4 family protein binding / positive regulation of gluconeogenesis / negative regulation of cytokine production involved in inflammatory response / 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) / cellular response to starvation / nuclear receptor binding / gluconeogenesis / respiratory electron transport chain / mitochondrion organization / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / negative regulation of smooth muscle cell proliferation / SUMOylation of intracellular receptors / negative regulation of transforming growth factor beta receptor signaling pathway / chromatin DNA binding / circadian regulation of gene expression / fatty acid metabolic process / wound healing / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / regulation of circadian rhythm / response to insulin / Cytoprotection by HMOX1 / PML body / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / Regulation of RUNX2 expression and activity / transcription coactivator binding / nuclear receptor activity / mRNA processing / : / positive regulation of cold-induced thermogenesis / heart development / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / cellular response to oxidative stress / protein-containing complex assembly / neuron apoptotic process / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more