[English] 日本語
Yorodumi
- PDB-6ms7: Peroxisome proliferator-activated receptor gamma ligand binding d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ms7
TitlePeroxisome proliferator-activated receptor gamma ligand binding domain in complex with a novel selective PPAR-gamma modulator VSP-77
Components
  • PGC1 LXXLL motif
  • Peroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / Peroxisome proliferator-activated receptor gamma / lignad binding domain / selective PPAR gamma modulator / VSP-77 / DNA BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of fatty acid oxidation / : / lncRNA binding / prostaglandin receptor activity / regulation of cholesterol transporter activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / response to muscle activity ...positive regulation of fatty acid oxidation / : / lncRNA binding / prostaglandin receptor activity / regulation of cholesterol transporter activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / response to muscle activity / negative regulation of vascular endothelial cell proliferation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonic acid binding / positive regulation of low-density lipoprotein receptor activity / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / DNA binding domain binding / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / STAT family protein binding / temperature homeostasis / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / LBD domain binding / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / E-box binding / alpha-actinin binding / intracellular glucose homeostasis / lipid homeostasis / response to starvation / fatty acid oxidation / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / response to dietary excess / negative regulation of macrophage derived foam cell differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / cell fate commitment / positive regulation of DNA binding / adipose tissue development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / BMP signaling pathway / long-chain fatty acid transport / energy homeostasis / nuclear retinoid X receptor binding / brown fat cell differentiation / regulation of cellular response to insulin stimulus / cell maturation / negative regulation of signaling receptor activity / positive regulation of gluconeogenesis / digestion / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / respiratory electron transport chain / mitochondrion organization / negative regulation of angiogenesis / RNA splicing / response to nutrient / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / negative regulation of MAP kinase activity / fatty acid metabolic process / Regulation of PTEN gene transcription / transcription coregulator binding / gluconeogenesis / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / negative regulation of smooth muscle cell proliferation / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / placenta development / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / lipid metabolic process / PPARA activates gene expression / chromatin DNA binding / mRNA processing
Similarity search - Function
PGC-1alpha, RNA recognition motif / PGC-1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / Retinoid X Receptor / Retinoid X Receptor / RNA recognition motif / RNA recognition motif ...PGC-1alpha, RNA recognition motif / PGC-1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / Retinoid X Receptor / Retinoid X 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 / Zinc finger, C4 type (two domains) / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
{[(1S)-1-(4-chlorophenyl)octyl]oxy}acetic acid / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.43 Å
AuthorsYi, W. / Jiang, H. / Zhou, X.E. / Shi, J. / Zhao, G. / Zhang, X. / Sun, Y. / Suino-Powell, K. / Li, J. / Li, J. ...Yi, W. / Jiang, H. / Zhou, X.E. / Shi, J. / Zhao, G. / Zhang, X. / Sun, Y. / Suino-Powell, K. / Li, J. / Li, J. / Melcher, K. / Xu, H.E.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81125023, 81502909 and 21877020 China
CitationJournal: Chem Sci / Year: 2020
Title: Identification and structural insight of an effective PPAR gamma modulator with improved therapeutic index for anti-diabetic drug discovery.
Authors: Jiang, H. / Zhou, X.E. / Shi, J. / Zhou, Z. / Zhao, G. / Zhang, X. / Sun, Y. / Suino-Powell, K. / Ma, L. / Gao, H. / Yu, X. / Li, J. / Li, J. / Melcher, K. / Xu, H.E. / Yi, W.
History
DepositionOct 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor gamma
B: PGC1 LXXLL motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0304
Polymers32,4332
Non-polymers5982
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-9 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.620, 53.890, 66.720
Angle α, β, γ (deg.)90.00, 107.24, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Peroxisome proliferator-activated receptor gamma / PPAR-gamma / Nuclear receptor subfamily 1 group C member 3


Mass: 31238.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli 042 (bacteria) / References: UniProt: P37231
#2: Protein/peptide PGC1 LXXLL motif


Mass: 1194.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q9UBK2*PLUS
#3: Chemical ChemComp-V77 / {[(1S)-1-(4-chlorophenyl)octyl]oxy}acetic acid


Mass: 298.805 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H23ClO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M of tri-sodium citrate (pH 5.5), 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 1.41→53.9 Å / Num. obs: 56329 / % possible obs: 98.7 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.036 / Rrim(I) all: 0.069 / Net I/σ(I): 13.4
Reflection shellResolution: 1.41→1.49 Å

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.43→32.556 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.46
RfactorNum. reflection% reflection
Rfree0.208 3807 7.08 %
Rwork0.1856 --
obs0.1872 53782 98.34 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 1.43→32.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 0 272 2471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072275
X-RAY DIFFRACTIONf_angle_d1.143056
X-RAY DIFFRACTIONf_dihedral_angle_d16.708872
X-RAY DIFFRACTIONf_chiral_restr0.082353
X-RAY DIFFRACTIONf_plane_restr0.011383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.45920.32022110.32222848X-RAY DIFFRACTION96
1.4592-1.49090.30222160.27792881X-RAY DIFFRACTION97
1.4909-1.52560.28972180.24532888X-RAY DIFFRACTION97
1.5256-1.56380.25872140.23822897X-RAY DIFFRACTION97
1.5638-1.6060.26912100.2352893X-RAY DIFFRACTION97
1.606-1.65330.25462240.21062915X-RAY DIFFRACTION98
1.6533-1.70660.25542350.21062898X-RAY DIFFRACTION98
1.7066-1.76760.21262230.19432911X-RAY DIFFRACTION98
1.7676-1.83840.23092190.18912947X-RAY DIFFRACTION98
1.8384-1.92210.20922480.18532946X-RAY DIFFRACTION99
1.9221-2.02340.20322490.18412903X-RAY DIFFRACTION99
2.0234-2.15010.20292390.16882969X-RAY DIFFRACTION99
2.1501-2.31610.18732270.17152974X-RAY DIFFRACTION99
2.3161-2.54910.18362340.17512969X-RAY DIFFRACTION100
2.5491-2.91780.22251880.17853038X-RAY DIFFRACTION100
2.9178-3.67530.20222340.17683006X-RAY DIFFRACTION100
3.6753-32.56420.16772180.16283092X-RAY DIFFRACTION100

+
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://pdbjlvh1.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