[English] 日本語
Yorodumi
- PDB-9vzs: X-ray structure of human PPARalpha ligand binding domain-10-hydro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9vzs
TitleX-ray structure of human PPARalpha ligand binding domain-10-hydroxystearic acid (10-HSA) co-crystals obtained by cross-seeding
ComponentsPeroxisome proliferator-activated receptor alpha
KeywordsTRANSCRIPTION / Nuclear receptor / Protein-ligand complex / PPAR
Function / homology
Function and homology information


regulation of fatty acid transport / positive regulation of fatty acid beta-oxidation / regulation of ketone metabolic process / cellular response to fructose stimulus / negative regulation of hepatocyte apoptotic process / regulation of fatty acid metabolic process / negative regulation of cell growth involved in cardiac muscle cell development / lipoprotein metabolic process / positive regulation of fatty acid oxidation / negative regulation of appetite ...regulation of fatty acid transport / positive regulation of fatty acid beta-oxidation / regulation of ketone metabolic process / cellular response to fructose stimulus / negative regulation of hepatocyte apoptotic process / regulation of fatty acid metabolic process / negative regulation of cell growth involved in cardiac muscle cell development / lipoprotein metabolic process / positive regulation of fatty acid oxidation / negative regulation of appetite / behavioral response to nicotine / negative regulation of leukocyte cell-cell adhesion / mitogen-activated protein kinase kinase kinase binding / ubiquitin conjugating enzyme binding / negative regulation of glycolytic process / positive regulation of fatty acid metabolic process / NFAT protein binding / DNA-binding transcription activator activity / negative regulation of cholesterol storage / nuclear steroid receptor activity / positive regulation of ATP biosynthetic process / negative regulation of macrophage derived foam cell differentiation / positive regulation of lipid biosynthetic process / lactation / phosphatase binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / negative regulation of blood pressure / hormone-mediated signaling pathway / intracellular receptor signaling pathway / nitric oxide metabolic process / negative regulation of reactive oxygen species biosynthetic process / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of cytokine production involved in inflammatory response / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Activation of gene expression by SREBF (SREBP) / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / MDM2/MDM4 family protein binding / negative regulation of miRNA transcription / fatty acid metabolic process / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to starvation / SUMOylation of intracellular receptors / circadian regulation of gene expression / RNA polymerase II transcription regulator complex / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / negative regulation of inflammatory response / response to insulin / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / fibrillar center / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear receptor activity / regulation of circadian rhythm / transcription coactivator binding / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / defense response to virus / sequence-specific DNA binding / response to hypoxia / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / lipid binding / positive regulation of DNA-templated transcription / protein-containing complex binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / DNA-templated transcription / nucleoplasm / zinc ion binding / nucleus
Similarity search - Function
Peroxisome proliferator-activated receptor alpha / 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 ...Peroxisome proliferator-activated receptor alpha / 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
(10R)-10-hydroxyoctadecanoic acid / Peroxisome proliferator-activated receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.455 Å
AuthorsLiu, J. / Krause, H.M. / Kamata, S. / Honda, A. / Watase, K. / 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: Nat Microbiol / Year: 2026
Title: Microbial 10-oxostearic acid protects mice against colitis via the nuclear receptor PPAR alpha.
Authors: Liu, J. / Li, H. / Tian, Y. / Guo, M. / Sahin, C. / Kamata, S. / Honda, A. / Campbell, J. / Shi, J. / Yurtal, E.D. / Yang, D. / Jachimowicz, M. / Hu, S. / Gong, Y. / Navarre, W. / Ishii, I. ...Authors: Liu, J. / Li, H. / Tian, Y. / Guo, M. / Sahin, C. / Kamata, S. / Honda, A. / Campbell, J. / Shi, J. / Yurtal, E.D. / Yang, D. / Jachimowicz, M. / Hu, S. / Gong, Y. / Navarre, W. / Ishii, I. / Cummins, C.L. / Peng, H. / Wang, S. / Wang, X. / Mani, S. / Krause, H.M.
History
DepositionJul 23, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2493
Polymers30,8561
Non-polymers3932
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-0 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.667, 61.361, 53.081
Angle α, β, γ (deg.)90.00, 106.67, 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) / Production host: Escherichia coli (E. coli) / References: UniProt: Q07869
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-WAD / (10R)-10-hydroxyoctadecanoic acid / (R)-10-Hydroxystearic acid


Mass: 300.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.1M HEPES (pH 7.0), 25% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 27, 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: 1.45→42.79 Å / Num. obs: 46538 / % possible obs: 96.4 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.021 / Rrim(I) all: 0.04 / Net I/σ(I): 18.7 / Num. measured all: 160879
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2185 / CC1/2: 0.897 / Rpim(I) all: 0.224 / Rrim(I) all: 0.407

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.11.1-2575-000refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.455→39.154 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 19.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2012 4410 4.91 %
Rwork0.1828 --
obs0.1837 46530 94.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.455→39.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2093 0 27 139 2259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052291
X-RAY DIFFRACTIONf_angle_d0.7383100
X-RAY DIFFRACTIONf_dihedral_angle_d14.395884
X-RAY DIFFRACTIONf_chiral_restr0.06351
X-RAY DIFFRACTIONf_plane_restr0.004398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.455-1.47120.31021190.24412526X-RAY DIFFRACTION83
1.4712-1.48850.25831490.24732799X-RAY DIFFRACTION93
1.4885-1.50660.24921700.22532731X-RAY DIFFRACTION93
1.5066-1.52570.26881500.20972739X-RAY DIFFRACTION93
1.5257-1.54580.23391540.21332823X-RAY DIFFRACTION93
1.5458-1.5670.22371180.19092770X-RAY DIFFRACTION93
1.567-1.58930.22351260.19272889X-RAY DIFFRACTION94
1.5893-1.61310.22541730.18982809X-RAY DIFFRACTION93
1.6131-1.63830.20121490.18272837X-RAY DIFFRACTION94
1.6383-1.66510.1891490.1912788X-RAY DIFFRACTION93
1.6651-1.69380.20141570.19182817X-RAY DIFFRACTION94
1.6938-1.72460.23941550.17672867X-RAY DIFFRACTION95
1.7246-1.75780.22151400.19432813X-RAY DIFFRACTION94
1.7578-1.79370.25691470.19232837X-RAY DIFFRACTION95
1.7937-1.83270.21441580.19032883X-RAY DIFFRACTION95
1.8327-1.87530.23041350.1842877X-RAY DIFFRACTION95
1.8753-1.92220.23451250.18482892X-RAY DIFFRACTION96
1.9222-1.97420.16341280.17712926X-RAY DIFFRACTION95
1.9742-2.03230.20951480.19332877X-RAY DIFFRACTION96
2.0323-2.09790.19571480.19042836X-RAY DIFFRACTION96
2.0979-2.17280.15981540.1732915X-RAY DIFFRACTION96
2.1728-2.25980.18321540.17752877X-RAY DIFFRACTION96
2.2598-2.36270.22821390.17822926X-RAY DIFFRACTION96
2.3627-2.48720.21111390.18782893X-RAY DIFFRACTION97
2.4872-2.6430.24091760.18762886X-RAY DIFFRACTION96
2.643-2.8470.18781630.19182896X-RAY DIFFRACTION97
2.847-3.13340.19311360.2012945X-RAY DIFFRACTION97
3.1334-3.58660.1921410.17952903X-RAY DIFFRACTION97
3.5866-4.51770.16941700.15472907X-RAY DIFFRACTION97
4.5177-39.1540.191400.16752949X-RAY DIFFRACTION98

+
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