[English] 日本語
Yorodumi
- PDB-5two: Peroxisome proliferator-activated receptor gamma ligand binding d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5two
TitlePeroxisome proliferator-activated receptor gamma ligand binding domain in complex with a novel selectively PPAR gamma-modulating ligand VSP-51
Components
  • PRO-SER-LEU-LEU-LYS-LYS-LEU-LEU-LEU-ALA-PRO
  • Peroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / Peroxisome proliferator-activated receptor gamma / lignad binding domain / selective PPAR gamma ligand / VSP-51 / DNA BINDING PROTEIN
Function / homology
Function and homology information


Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / cellular respiration / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / beige fat cell differentiation / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly ...Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / cellular respiration / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / prostaglandin receptor activity / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / beige fat cell differentiation / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / : / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / arachidonate binding / positive regulation of adiponectin secretion / DNA binding domain binding / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of cardiac muscle hypertrophy in response to stress / response to starvation / positive regulation of fatty acid metabolic process / STAT family protein binding / positive regulation of lipid metabolic process / WW domain binding / response to lipid / response to muscle activity / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / temperature homeostasis / negative regulation of cholesterol storage / positive regulation of lipoprotein transport / lncRNA binding / negative regulation of SMAD protein signal transduction / response to dietary excess / fatty acid oxidation / lipid homeostasis / intracellular glucose homeostasis / E-box binding / alpha-actinin binding / R-SMAD binding / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of blood vessel endothelial cell migration / white fat cell differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / positive regulation of cholesterol efflux / monocyte differentiation / negative regulation of BMP signaling pathway / cell fate commitment / adipose tissue development / cellular response to low-density lipoprotein particle stimulus / BMP signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of mitochondrial fission / negative regulation of osteoblast differentiation / long-chain fatty acid transport / positive regulation of fat cell differentiation / nuclear retinoid X receptor binding / fat cell differentiation / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / energy homeostasis / digestion / negative regulation of MAPK cascade / intracellular receptor signaling pathway / cell maturation / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / epithelial cell differentiation / peptide binding / positive regulation of adipose tissue development / regulation of cellular response to insulin stimulus / response to nutrient / positive regulation of gluconeogenesis / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / RNA splicing / brown fat cell differentiation / placenta development / negative regulation of angiogenesis / Regulation of PTEN gene transcription / nuclear receptor binding / transcription coregulator binding / gluconeogenesis / positive regulation of apoptotic signaling pathway / respiratory electron transport chain / transcription coregulator activity / SUMOylation of intracellular receptors / transcription initiation at RNA polymerase II promoter / circadian regulation of gene expression / negative regulation of smooth muscle cell proliferation / mitochondrion organization / Heme signaling / negative regulation of transforming growth factor beta receptor signaling pathway / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / fatty acid metabolic process / regulation of circadian rhythm / chromatin DNA binding / PML body
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 ...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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7MV / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.927 Å
AuthorsYi, W. / Shi, J. / Zhao, G. / Zhou, X.E. / Suino-Powell, K. / Melcher, K. / Xu, H.E.
Funding support China, 2items
OrganizationGrant numberCountry
Youth Innovation Promotion Association CAS, the Shanghai Municipal Natural Science Foundation15ZR1447800 China
the Chinese Postdoctoral Science Foundation2014M560363 China
CitationJournal: Sci Rep / Year: 2017
Title: Identification of a novel selective PPAR gamma ligand with a unique binding mode and improved therapeutic profile in vitro.
Authors: Yi, W. / Shi, J. / Zhao, G. / Zhou, X.E. / Suino-Powell, K. / Melcher, K. / Xu, H.E.
History
DepositionNov 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: PRO-SER-LEU-LEU-LYS-LYS-LEU-LEU-LEU-ALA-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0823
Polymers32,6892
Non-polymers3931
Water2,234124
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-9 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.893, 88.504, 122.163
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-695-

HOH

-
Components

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


Mass: 31094.135 Da / Num. of mol.: 1 / Fragment: lignad binding domain (UNP residues 234-505)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli (E. coli) / References: UniProt: P37231
#2: Protein/peptide PRO-SER-LEU-LEU-LYS-LYS-LEU-LEU-LEU-ALA-PRO


Mass: 1594.932 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others) / References: UniProt: Q9UBK2*PLUS
#3: Chemical ChemComp-7MV / N-benzyl-1-[(4-chloro-3-fluorophenyl)methyl]-1H-indole-5-carboxamide


Mass: 392.853 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H18ClFN2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 0.1 M of tri-sodium citrate (pH 5.5), 20% w/v PEG 3350
PH range: 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 23586 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.031 / Net I/σ(I): 26.6
Reflection shellResolution: 1.92→1.95 Å / Rmerge(I) obs: 0.792 / Rrim(I) all: 0.317

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U9Q

3u9q


Resolution: 1.927→37.672 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2365 1584 6.72 %
Rwork0.2087 --
obs0.2107 23586 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.927→37.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 28 124 2395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082312
X-RAY DIFFRACTIONf_angle_d1.1433116
X-RAY DIFFRACTIONf_dihedral_angle_d11.737880
X-RAY DIFFRACTIONf_chiral_restr0.039361
X-RAY DIFFRACTIONf_plane_restr0.005390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9272-1.96650.3525710.30171221X-RAY DIFFRACTION93
1.9665-2.00930.3812920.29171267X-RAY DIFFRACTION100
2.0093-2.0560.27850.25261275X-RAY DIFFRACTION100
2.056-2.10740.2553870.22791317X-RAY DIFFRACTION100
2.1074-2.16440.2475910.24661259X-RAY DIFFRACTION100
2.1644-2.22810.2793800.23451301X-RAY DIFFRACTION100
2.2281-2.30.28651020.23221290X-RAY DIFFRACTION100
2.3-2.38220.298900.2241292X-RAY DIFFRACTION100
2.3822-2.47750.2548910.23081286X-RAY DIFFRACTION100
2.4775-2.59030.26121010.23731288X-RAY DIFFRACTION100
2.5903-2.72680.2513980.23311278X-RAY DIFFRACTION100
2.7268-2.89760.27031110.21721291X-RAY DIFFRACTION100
2.8976-3.12120.2835850.2351299X-RAY DIFFRACTION100
3.1212-3.43510.23291170.22551289X-RAY DIFFRACTION100
3.4351-3.93170.2219880.18471320X-RAY DIFFRACTION100
3.9317-4.95180.1928900.16681343X-RAY DIFFRACTION100
4.9518-37.6790.18131050.17731386X-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