[English] 日本語
Yorodumi
- PDB-3tkm: Crystal structure PPAR delta binding GW0742 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tkm
TitleCrystal structure PPAR delta binding GW0742
ComponentsPeroxisome proliferator-activated receptor delta
KeywordsTRANSCRIPTION/TRANSCRIPTION ACTIVATOR / nuclear receptor / TRANSCRIPTION / TRANSCRIPTION-TRANSCRIPTION ACTIVATOR complex
Function / homology
Function and homology information


fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process ...fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process / Carnitine metabolism / negative regulation of myoblast differentiation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of fatty acid metabolic process / cell-substrate adhesion / fatty acid beta-oxidation / negative regulation of cholesterol storage / cellular response to nutrient levels / decidualization / keratinocyte proliferation / positive regulation of fat cell differentiation / fatty acid transport / adipose tissue development / energy homeostasis / embryo implantation / hormone-mediated signaling pathway / cholesterol metabolic process / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of miRNA transcription / fatty acid metabolic process / generation of precursor metabolites and energy / apoptotic signaling pathway / wound healing / lipid metabolic process / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / Nuclear Receptor transcription pathway / glucose metabolic process / nuclear receptor activity / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / cellular response to hypoxia / DNA-binding transcription factor binding / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / lipid binding / apoptotic process / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Peroxisome proliferator-activated receptor, beta / Peroxisome proliferator-activated receptor / Retinoid X Receptor / Retinoid X Receptor / 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 ...Peroxisome proliferator-activated receptor, beta / Peroxisome proliferator-activated receptor / Retinoid X Receptor / Retinoid X Receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-GW0 / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.953 Å
AuthorsTrivella, D.B.B. / Batista, F.H. / Polikarpov, I.
CitationJournal: Plos One / Year: 2012
Title: Structural Insights into Human Peroxisome Proliferator Activated Receptor Delta (PPAR-Delta) Selective Ligand Binding.
Authors: Batista, F.A. / Trivella, D.B. / Bernardes, A. / Gratieri, J. / Oliveira, P.S. / Figueira, A.C. / Webb, P. / Polikarpov, I.
History
DepositionAug 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Data collection / Database references / Derived calculations
Category: reflns / reflns_shell ...reflns / reflns_shell / struct_ref_seq_dif / struct_site
Item: _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value ..._reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value / _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 13, 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 delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9943
Polymers31,4311
Non-polymers5642
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.466, 74.766, 96.287
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Peroxisome proliferator-activated receptor delta / PPAR-delta / NUCI / Nuclear hormone receptor 1 / NUC1 / Nuclear receptor subfamily 1 group C member ...PPAR-delta / NUCI / Nuclear hormone receptor 1 / NUC1 / Nuclear receptor subfamily 1 group C member 2 / Peroxisome proliferator-activated receptor beta / PPAR-beta


Mass: 31430.535 Da / Num. of mol.: 1 / Fragment: LBD, UNP residues 171-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARD, NR1C2, PPARB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03181
#2: Chemical ChemComp-GW0 / {4-[({2-[3-fluoro-4-(trifluoromethyl)phenyl]-4-methyl-1,3-thiazol-5-yl}methyl)sulfanyl]-2-methylphenoxy}acetic acid / GW 0742


Mass: 471.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17F4NO3S2 / Comment: agonist*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.03 Å3/Da / Density % sol: 39.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 14% (w/v) polyethylene glycol (PEG) 8000, 200 mM KCl, 40 mM bis-Tris-propane (pH 9.5), 6% propanol, and 1 mM CaCl2 and detergent n-Octyl-b-D-thioglucoside (0.5 microliters in 5 microliters ...Details: 14% (w/v) polyethylene glycol (PEG) 8000, 200 mM KCl, 40 mM bis-Tris-propane (pH 9.5), 6% propanol, and 1 mM CaCl2 and detergent n-Octyl-b-D-thioglucoside (0.5 microliters in 5 microliters drops), VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4589 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 20, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4589 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 19254 / Num. obs: 19254 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.098 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsRsym valueDiffraction-ID% possible all
1.95-2.024.72.6318800.4381100
2.02-2.14.93.119740.3971100
2.1-2.25.54.3118910.2961100
2.2-2.315.84.9518710.2881100
2.31-2.466.17.0719080.2151100
2.46-2.656.36.3819260.2181100
2.65-2.916.39.5419290.1771100
2.91-3.336.16.919380.1441100
3.33-4.26.114.9119550.091100
4.2-305.817.2420820.071100

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 2009_06_19_0104)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ET2

3et2


Resolution: 1.953→24.352 Å / SU ML: 0.26 / Isotropic thermal model: overall / σ(F): 1.34 / Phase error: 24.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 977 5.1 %random
Rwork0.1969 ---
obs0.1993 19139 99.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.547 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3203 Å20 Å2-0 Å2
2--0.4335 Å2-0 Å2
3----0.7538 Å2
Refinement stepCycle: LAST / Resolution: 1.953→24.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 37 158 2365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032376
X-RAY DIFFRACTIONf_angle_d0.7723235
X-RAY DIFFRACTIONf_dihedral_angle_d15.035904
X-RAY DIFFRACTIONf_chiral_restr0.046362
X-RAY DIFFRACTIONf_plane_restr0.003409
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.953-2.05550.30291350.2532519251998
2.0555-2.18420.29931250.23262556255699
2.1842-2.35280.26541310.21892578257899
2.3528-2.58930.29091440.204325662566100
2.5893-2.96340.25361510.203925912591100
2.9634-3.73140.25271490.18572599259999
3.7314-24.35360.19181420.17332753275399

+
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