[English] 日本語
Yorodumi
- PDB-1gwx: MOLECULAR RECOGNITION OF FATTY ACIDS BY PEROXISOME PROLIFERATOR-A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gwx
TitleMOLECULAR RECOGNITION OF FATTY ACIDS BY PEROXISOME PROLIFERATOR-ACTIVATED RECEPTORS
ComponentsPROTEIN (PPAR-DELTA)
KeywordsTRANSCRIPTION / PPAR / FATTY ACIDS / NUCLEAR RECEPTOR FOLD
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 / positive regulation of epidermis development / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / D-glucose transmembrane transport / negative regulation of smooth muscle cell migration ...fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / positive regulation of epidermis development / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / D-glucose transmembrane transport / negative regulation of smooth muscle cell migration / positive regulation of myoblast proliferation / proteoglycan metabolic process / fatty acid catabolic process / negative regulation of collagen biosynthetic process / positive regulation of fatty acid oxidation / phospholipid biosynthetic process / Carnitine shuttle / negative regulation of myoblast differentiation / response to vitamin A / Signaling by Retinoic Acid / positive regulation of fatty acid metabolic process / nuclear steroid receptor activity / fatty acid beta-oxidation / negative regulation of cholesterol storage / cell-substrate adhesion / positive regulation of insulin secretion involved in cellular response to glucose stimulus / decidualization / keratinocyte proliferation / positive regulation of fat cell differentiation / adipose tissue development / NF-kappaB binding / cellular response to nutrient levels / fatty acid transport / response to glucose / energy homeostasis / intracellular receptor signaling pathway / hormone-mediated signaling pathway / embryo implantation / cholesterol metabolic process / negative regulation of miRNA transcription / response to activity / fatty acid metabolic process / generation of precursor metabolites and energy / phosphatidylinositol 3-kinase/protein kinase B signal transduction / apoptotic signaling pathway / negative regulation of smooth muscle cell proliferation / wound healing / transcription coactivator binding / negative regulation of cell growth / Nuclear Receptor transcription pathway / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / nuclear receptor activity / glucose metabolic process / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / vasodilation / heart development / cellular response to lipopolysaccharide / cellular response to hypoxia / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / apoptotic process / lipid binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / 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 / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. ...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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-433 / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsXu, H.E. / Lambert, M.H. / Montana, V.G. / Park, D.J. / Blanchard, S. / Brown, P. / Sternbach, D. / Lehmann, J. / Bruce, G.W. / Willson, T.M. ...Xu, H.E. / Lambert, M.H. / Montana, V.G. / Park, D.J. / Blanchard, S. / Brown, P. / Sternbach, D. / Lehmann, J. / Bruce, G.W. / Willson, T.M. / Kliewer, S.A. / Milburn, M.V.
CitationJournal: Mol.Cell / Year: 1999
Title: Molecular recognition of fatty acids by peroxisome proliferator-activated receptors.
Authors: Xu, H.E. / Lambert, M.H. / Montana, V.G. / Parks, D.J. / Blanchard, S.G. / Brown, P.J. / Sternbach, D.D. / Lehmann, J.M. / Wisely, G.B. / Willson, T.M. / Kliewer, S.A. / Milburn, M.V.
History
DepositionMar 17, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (PPAR-DELTA)
B: PROTEIN (PPAR-DELTA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1984
Polymers62,0342
Non-polymers1,1642
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.250, 94.900, 96.200
Angle α, β, γ (deg.)90.00, 98.00, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein PROTEIN (PPAR-DELTA)


Mass: 31017.061 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARD / Plasmid: PSETA WITH T7 PROMOTER / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE30) / References: UniProt: Q03181
#2: Chemical ChemComp-433 / 2-(4-{3-[1-[2-(2-CHLORO-6-FLUORO-PHENYL)-ETHYL]-3-(2,3-DICHLORO-PHENYL)-UREIDO]-PROPYL}-PHENOXY)-2-METHYL-PROPIONIC ACID / GW2433


Mass: 581.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H28Cl3FN2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal growpH: 9 / Details: pH 9.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mMbis-tris-propandiol1reservoir
210 mMdithiothreitol1reservoir
32.5 %propandiol1reservoir
41 mMEDTA1reservoir
50.5 %heptyl-beta-D-glucopyranoside1reservoir
60.2 mM1reservoirKCl
75 %PEG80001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. obs: 40000 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. obs: 22731 / % possible obs: 94.5 % / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
Mean I/σ(I) obs: 2.3

-
Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 1262531.98 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.303 1751 10.2 %RANDOM
Rwork0.246 ---
obs-17219 73.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 94.38 Å2 / ksol: 0.533 e/Å3
Displacement parametersBiso mean: 57 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å22.17 Å2
2--2.09 Å20 Å2
3----3.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4330 0 76 87 4493
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.99
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.691.5
X-RAY DIFFRACTIONx_mcangle_it4.362
X-RAY DIFFRACTIONx_scbond_it3.942
X-RAY DIFFRACTIONx_scangle_it5.62.5
LS refinement shellResolution: 2.5→2.65 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 143 11.4 %
Rwork0.281 1107 -
obs--32.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM433.TOP
X-RAY DIFFRACTION3433.PAR
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.2 % / Rfactor obs: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 57 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.326 / % reflection Rfree: 11.4 % / Rfactor Rwork: 0.281

+
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