[English] 日本語
Yorodumi
- PDB-9iwm: X-ray structure of human PPARalpha ligand binding domain-GW7647-T... -

+
Open data


ID or keywords:

Loading...

-
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 / G0 to G1 transition ...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 / G0 to G1 transition / mammary gland branching involved in thelarche / thyroid hormone receptor signaling pathway / positive regulation of fatty acid beta-oxidation / cellular response to fructose stimulus / regulation of ketone metabolic process / regulation of fatty acid metabolic process / core mediator complex / negative regulation of cell growth involved in cardiac muscle cell development / regulation of vitamin D receptor signaling pathway / negative regulation of appetite / negative regulation of hepatocyte apoptotic process / lipoprotein metabolic process / positive regulation of fatty acid oxidation / behavioral response to nicotine / nuclear retinoic acid receptor binding / ventricular trabecula myocardium morphogenesis / mediator complex / positive regulation of keratinocyte differentiation / negative regulation of leukocyte cell-cell adhesion / thyroid hormone generation / Generic Transcription Pathway / peroxisome proliferator activated receptor binding / embryonic heart tube development / cellular response to thyroid hormone stimulus / negative regulation of glycolytic process / positive regulation of hepatocyte proliferation / ubiquitin conjugating enzyme binding / nuclear vitamin D receptor binding / embryonic hindlimb morphogenesis / nuclear thyroid hormone receptor binding / lens development in camera-type eye / mitogen-activated protein kinase kinase kinase binding / embryonic hemopoiesis / megakaryocyte development / positive regulation of fatty acid metabolic process / cellular response to hepatocyte growth factor stimulus / cellular response to steroid hormone stimulus / positive regulation of intracellular estrogen receptor signaling pathway / DNA-binding transcription activator activity / histone acetyltransferase binding / LBD domain binding / NFAT protein binding / epithelial cell proliferation involved in mammary gland duct elongation / negative regulation of cholesterol storage / RSV-host interactions / erythrocyte development / fat cell differentiation / mammary gland branching involved in pregnancy / positive regulation of ATP biosynthetic process / nuclear steroid receptor activity / monocyte differentiation / negative regulation of macrophage derived foam cell differentiation / general transcription initiation factor binding / animal organ regeneration / epidermis development / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / ubiquitin ligase complex / negative regulation of keratinocyte proliferation / positive regulation of transcription initiation by RNA polymerase II / embryonic placenta development / nuclear receptor-mediated steroid hormone signaling pathway / 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 / nitric oxide metabolic process / lactation / hormone-mediated signaling pathway / negative regulation of blood pressure / negative regulation of reactive oxygen species biosynthetic process / : / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / MDM2/MDM4 family protein binding / positive regulation of gluconeogenesis / response to nutrient / 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 / Activation of gene expression by SREBF (SREBP) / cellular response to epidermal growth factor stimulus / positive regulation of erythrocyte differentiation / cellular response to starvation / nuclear estrogen receptor binding / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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