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- PDB-4ci4: Structural basis for GL479 a dual Peroxisome Proliferator-Activat... -

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Basic information

Entry
Database: PDB / ID: 4ci4
TitleStructural basis for GL479 a dual Peroxisome Proliferator-Activated Receptor alpha agonist
ComponentsPEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHA
KeywordsTRANSFERASE / DUAL AGONIST / PPAR / NUCLEAR RECEPTOR / GL479
Function / homology
Function and homology information


positive regulation of transformation of host cell by virus / regulation of fatty acid transport / regulation of fatty acid metabolic process / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of fatty acid oxidation / regulation of cellular ketone metabolic process / cellular response to fructose stimulus / behavioral response to nicotine / negative regulation of appetite ...positive regulation of transformation of host cell by virus / regulation of fatty acid transport / regulation of fatty acid metabolic process / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of fatty acid oxidation / regulation of cellular ketone metabolic process / cellular response to fructose stimulus / behavioral response to nicotine / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / lipoprotein metabolic process / negative regulation of hepatocyte apoptotic process / mitogen-activated protein kinase kinase kinase binding / negative regulation of leukocyte cell-cell adhesion / ubiquitin conjugating enzyme binding / negative regulation of glycolytic process / negative regulation of sequestering of triglyceride / nuclear steroid receptor activity / DNA-binding transcription activator activity / positive regulation of fatty acid metabolic process / nitric oxide metabolic process / positive regulation of ATP biosynthetic process / NFAT protein binding / negative regulation of cholesterol storage / negative regulation of macrophage derived foam cell differentiation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of cytokine production involved in inflammatory response / epidermis development / phosphatase binding / MDM2/MDM4 family protein binding / positive regulation of lipid biosynthetic process / negative regulation of signaling receptor activity / negative regulation of reactive oxygen species biosynthetic process / positive regulation of gluconeogenesis / RORA activates gene expression / cellular response to starvation / negative regulation of blood pressure / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian gene expression / fatty acid metabolic process / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / gluconeogenesis / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / response to insulin / SUMOylation of intracellular receptors / Heme signaling / wound healing / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / nuclear receptor activity / Circadian Clock / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / lipid binding / chromatin / protein-containing complex binding / 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 alpha / 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 alpha / 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-Y1N / Peroxisome proliferator-activated receptor alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 Å
AuthorsSantos, J.C. / Bernardes, A. / Polikarpov, I.
CitationJournal: J. Struct. Biol. / Year: 2015
Title: Different binding and recognition modes of GL479, a dual agonist of Peroxisome Proliferator-Activated Receptor alpha / gamma.
Authors: dos Santos, J.C. / Bernardes, A. / Giampietro, L. / Ammazzalorso, A. / De Filippis, B. / Amoroso, R. / Polikarpov, I.
History
DepositionDec 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Sep 9, 2015Group: Database references
Revision 1.3Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4212
Polymers31,0161
Non-polymers4041
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.526, 64.526, 124.387
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHA / PPAR-ALPHA / NUCLEAR RECEPTOR SUBFAMILY 1 GROUP C MEMBER 1


Mass: 31016.131 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, RESDIUES 195-468
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07869, histone acetyltransferase
#2: Chemical ChemComp-Y1N / 2-methyl-2-[4-[2-[4-[(E)-phenyldiazenyl]phenoxy]ethyl]phenoxy]propanoic acid


Mass: 404.458 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H24N2O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.14 % / Description: NONE
Crystal growDetails: 27% PEG 20000, 0.1 M TRIS-HCL PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.3→44.78 Å / Num. obs: 22478 / % possible obs: 99.7 % / Observed criterion σ(I): 2.2 / Redundancy: 2.9 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.2 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BCR

4bcr


Resolution: 2.302→44.779 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 29.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 580 4.8 %
Rwork0.2148 --
obs0.2169 12191 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.302→44.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 30 52 2023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082008
X-RAY DIFFRACTIONf_angle_d1.12712
X-RAY DIFFRACTIONf_dihedral_angle_d15.908743
X-RAY DIFFRACTIONf_chiral_restr0.072313
X-RAY DIFFRACTIONf_plane_restr0.004343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.302-2.53360.31481450.24812808X-RAY DIFFRACTION99
2.5336-2.90020.34251340.2622852X-RAY DIFFRACTION100
2.9002-3.65370.25341430.22222911X-RAY DIFFRACTION100
3.6537-44.78780.22841580.19173040X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.9774-1.76440.88112.4684-1.28827.1843-0.4324-0.44092.0691-0.93770.677-1.2152-1.8401-0.3198-0.25750.9926-0.1410.10590.3693-0.07470.7798-24.609121.8863-6.7517
25.9957-2.30712.58264.0780.63574.6105-0.7561-1.23310.23230.66831.4195-0.7479-0.42821.4651-0.31440.59460.0823-0.0070.9225-0.35470.6225-8.385112.12124.9758
34.35863.3643-3.65564.409-3.32253.32860.4892-2.640.62140.09650.1571.4106-0.44822.1241-0.24211.05230.3103-0.22591.6022-0.1960.7398-7.96373.328720.9467
43.1096-0.8746-1.96733.8473-0.41074.9373-0.5325-0.562-0.10230.40180.5846-0.00660.17450.0552-0.10090.35440.11180.01960.475-0.01790.2651-28.3268.54184.4408
53.983-2.206-0.4593.23180.44464.3333-0.427-0.7306-0.2520.36540.7901-0.31560.36811.0348-0.22930.43130.1473-0.02770.6912-0.13380.4447-13.76962.43881.5102
62.7988-3.1319-3.20286.5743-0.57089.96290.48311.6661-0.0716-0.5191-0.66840.83021.1851-0.87980.26040.5889-0.1738-0.09550.82790.02560.5855-38.85164.8706-6.3035
72.50221.4768-3.31453.0134-1.08827.123-0.50731.43090.5627-0.64250.46250.2456-0.1781-0.3923-0.0590.64860.0174-0.04540.54790.04920.4065-26.538212.5291-16.8133
84.3953.3492-2.80138.1338-6.25237.827-0.40280.1135-0.8211-0.29750.3250.27930.6135-0.5251-0.01050.46040.00660.06840.30150.01550.4888-24.6067-3.0873-3.0584
95.2554-1.4342.08063.2637-4.79367.3311-0.1417-0.6951-0.79620.7248-0.24750.69352.06750.79210.22450.88460.20550.14940.580.08440.5288-31.3137-1.024613.3016
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 204 THROUGH 217 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 218 THROUGH 243 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 244 THROUGH 268 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 269 THROUGH 324 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 325 THROUGH 383 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 384 THROUGH 393 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 394 THROUGH 421 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 422 THROUGH 450 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 451 THROUGH 467 )

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