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- PDB-7e5f: HUMAN PPAR ALPHA LIGAND BINDING DOMAIN IN COMPLEX WITH TIPP703 OB... -

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Basic information

Entry
Database: PDB / ID: 7e5f
TitleHUMAN PPAR ALPHA LIGAND BINDING DOMAIN IN COMPLEX WITH TIPP703 OBTAINED BY SOAKING
ComponentsPeroxisome proliferator-activated receptor alpha
KeywordsTRANSCRIPTION / NUCLEAR RECEPTOR / PPAR / PROTEIN-LIGAND COMPLEX
Function / homology
Function and homology information


positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / regulation of ketone metabolic process / cellular response to fructose stimulus / regulation of fatty acid metabolic process / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / lipoprotein metabolic process ...positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / regulation of ketone metabolic process / cellular response to fructose stimulus / regulation of fatty acid metabolic process / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / lipoprotein metabolic process / positive regulation of fatty acid oxidation / behavioral response to nicotine / negative regulation of hepatocyte apoptotic process / negative regulation of leukocyte cell-cell adhesion / mitogen-activated protein kinase kinase kinase binding / ubiquitin conjugating enzyme binding / negative regulation of glycolytic process / positive regulation of fatty acid metabolic process / DNA-binding transcription activator activity / nuclear steroid receptor activity / positive regulation of ATP biosynthetic process / NFAT protein binding / negative regulation of cholesterol storage / negative regulation of macrophage derived foam cell differentiation / epidermis development / phosphatase binding / positive regulation of lipid biosynthetic process / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / intracellular receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / nitric oxide metabolic process / negative regulation of blood pressure / hormone-mediated signaling pathway / : / MDM2/MDM4 family protein binding / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / negative regulation of cytokine production involved in inflammatory response / response to nutrient / positive regulation of gluconeogenesis / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / cellular response to starvation / gluconeogenesis / fatty acid metabolic process / response to insulin / SUMOylation of intracellular receptors / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / wound healing / Heme signaling / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / PPARA activates gene expression / regulation of circadian rhythm / Cytoprotection by HMOX1 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / nuclear receptor activity / : / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / response to ethanol / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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 / : / 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 ...Peroxisome proliferator-activated receptor alpha / Peroxisome proliferator-activated 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
Similarity search - Domain/homology
Chem-S44 / Peroxisome proliferator-activated receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsOyama, T. / Kamata, S. / Ishii, I. / Miyachi, H.
CitationJournal: Biol.Pharm.Bull. / Year: 2021
Title: Crystal Structures of the Human Peroxisome Proliferator-Activated Receptor (PPAR) alpha Ligand-Binding Domain in Complexes with a Series of Phenylpropanoic Acid Derivatives Generated by a ...Title: Crystal Structures of the Human Peroxisome Proliferator-Activated Receptor (PPAR) alpha Ligand-Binding Domain in Complexes with a Series of Phenylpropanoic Acid Derivatives Generated by a Ligand-Exchange Soaking Method.
Authors: Oyama, T. / Kamata, S. / Ishii, I. / Miyachi, H.
History
DepositionFeb 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,3602
Polymers30,8561
Non-polymers5041
Water1,928107
1
A: Peroxisome proliferator-activated receptor alpha
hetero molecules

A: Peroxisome proliferator-activated receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7194
Polymers61,7122
Non-polymers1,0072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Unit cell
Length a, b, c (Å)44.893, 62.158, 53.369
Angle α, β, γ (deg.)90.000, 105.782, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Peroxisome proliferator-activated receptor alpha


Mass: 30856.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07869
#2: Chemical ChemComp-S44 / (2S)-2-(4-propoxy-3-{[({4-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]phenyl}carbonyl)amino]methyl}benzyl)butanoic acid / (S)-2-{3-[(4-adamantan-1-ylbenzoylamino)methyl]-4-propoxybenzyl} butyric acid


Mass: 503.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H41NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris, 25% (w/v) polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 21, 2017 / Details: two dimensional focusing mirror
RadiationMonochromator: fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 46821 / % possible obs: 98.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 25.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.022 / Rrim(I) all: 0.041 / Net I/σ(I): 12.3
Reflection shellResolution: 1.79→1.83 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1548 / CC1/2: 0.924 / Rpim(I) all: 0.214 / Rrim(I) all: 0.393 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2znn

2znn


Resolution: 1.79→43.2 Å / SU ML: 0.2256 / Cross valid method: FREE R-VALUE / σ(F): 0.38 / Phase error: 26.3489
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2288 2246 4.8 %
Rwork0.196 44575 -
obs0.1977 46821 89.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.38 Å2
Refinement stepCycle: LAST / Resolution: 1.79→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2085 0 37 107 2229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532186
X-RAY DIFFRACTIONf_angle_d0.78272954
X-RAY DIFFRACTIONf_chiral_restr0.0424338
X-RAY DIFFRACTIONf_plane_restr0.0054373
X-RAY DIFFRACTIONf_dihedral_angle_d12.0541839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.29951410.2742798X-RAY DIFFRACTION90.79
1.83-1.870.30461320.24812877X-RAY DIFFRACTION91.32
1.87-1.920.28861370.23952803X-RAY DIFFRACTION90.13
1.92-1.970.31311380.22882796X-RAY DIFFRACTION90.5
1.97-2.030.24031540.22462814X-RAY DIFFRACTION90.68
2.03-2.090.28071090.22692802X-RAY DIFFRACTION89.76
2.09-2.170.29261460.22992807X-RAY DIFFRACTION89.68
2.17-2.260.23891340.21572772X-RAY DIFFRACTION88.38
2.26-2.360.2431420.20452722X-RAY DIFFRACTION88.29
2.36-2.480.29371500.21632732X-RAY DIFFRACTION87.15
2.48-2.640.25291490.21962754X-RAY DIFFRACTION88.75
2.64-2.840.2771290.22922717X-RAY DIFFRACTION87.35
2.84-3.130.27461360.21792757X-RAY DIFFRACTION88.47
3.13-3.580.22111450.18752702X-RAY DIFFRACTION87.38
3.58-4.510.17761470.15262824X-RAY DIFFRACTION90.11
4.51-43.20.1641570.15652898X-RAY DIFFRACTION93.97

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