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- PDB-5hyk: Crystal structure of the complex PPARalpha/AL26-29 -

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Basic information

Entry
Database: PDB / ID: 5hyk
TitleCrystal structure of the complex PPARalpha/AL26-29
ComponentsPeroxisome proliferator-activated receptor alpha
KeywordsTRANSCRIPTION / Nuclear receptor / transcription factor / diabetes / bundle of alpha-helices
Function / homology
Function and homology information


positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / regulation of fatty acid metabolic process / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of fatty acid oxidation / cellular response to fructose stimulus / regulation of cellular ketone metabolic process / behavioral response to nicotine / negative regulation of appetite ...positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / regulation of fatty acid metabolic process / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of fatty acid oxidation / cellular response to fructose stimulus / regulation of cellular ketone metabolic process / 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 / nitric oxide metabolic process / positive regulation of fatty acid 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 cytokine production involved in inflammatory response / epidermis development / phosphatase binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of lipid biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of signaling receptor activity / MDM2/MDM4 family protein binding / positive regulation of gluconeogenesis / RORA activates gene expression / negative regulation of blood pressure / Regulation of lipid metabolism by PPARalpha / cellular response to starvation / hormone-mediated signaling pathway / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian gene expression / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / fatty acid metabolic process / gluconeogenesis / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / wound healing / Heme signaling / SUMOylation of intracellular receptors / response to insulin / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / Cytoprotection by HMOX1 / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / 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 / DNA-binding transcription factor binding / response to ethanol / 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 / protein-containing complex binding / 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 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-65W / Peroxisome proliferator-activated receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsPochetti, G. / Montanari, R. / Capelli, D. / Loiodice, F. / Laghezza, A. / Lavecchia, A.
CitationJournal: Sci Rep / Year: 2016
Title: Structural basis for PPAR partial or full activation revealed by a novel ligand binding mode.
Authors: Capelli, D. / Cerchia, C. / Montanari, R. / Loiodice, F. / Tortorella, P. / Laghezza, A. / Cervoni, L. / Pochetti, G. / Lavecchia, A.
History
DepositionFeb 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0312
Polymers30,7251
Non-polymers3061
Water3,981221
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.650, 63.650, 126.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-692-

HOH

21A-698-

HOH

31A-753-

HOH

41A-754-

HOH

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Components

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


Mass: 30724.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARA, NR1C1, PPAR / Production host: Escherichia coli (E. coli) / References: UniProt: Q07869
#2: Chemical ChemComp-65W / 2-methyl-2-[4-(naphthalen-1-yl)phenoxy]propanoic acid


Mass: 306.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 3350 20%, 0,2 M Mg acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.83→36.622 Å / Num. obs: 23665 / % possible obs: 100 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 22.7
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
iMOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VI8

3vi8


Resolution: 1.83→36.622 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 25.58
RfactorNum. reflection% reflection
Rfree0.2618 1140 4.83 %
Rwork0.2112 --
obs0.2137 23595 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.83→36.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 23 221 2281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072115
X-RAY DIFFRACTIONf_angle_d1.0952852
X-RAY DIFFRACTIONf_dihedral_angle_d14.195800
X-RAY DIFFRACTIONf_chiral_restr0.045326
X-RAY DIFFRACTIONf_plane_restr0.005360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8301-1.91330.34541230.24742741X-RAY DIFFRACTION100
1.9133-2.01420.25251350.22012762X-RAY DIFFRACTION100
2.0142-2.14040.30581370.2132761X-RAY DIFFRACTION100
2.1404-2.30560.24221400.20912757X-RAY DIFFRACTION100
2.3056-2.53760.26191370.21192791X-RAY DIFFRACTION100
2.5376-2.90470.24731430.22342810X-RAY DIFFRACTION100
2.9047-3.65910.26841490.21112837X-RAY DIFFRACTION100
3.6591-36.62930.25221760.19932996X-RAY DIFFRACTION100

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