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- PDB-7e5h: HUMAN PPAR ALPHA LIGAND BINDING DOMAIN IN COMPLEX WITH APHM6 OBTA... -

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Basic information

Entry
Database: PDB / ID: 7e5h
TitleHUMAN PPAR ALPHA LIGAND BINDING DOMAIN IN COMPLEX WITH APHM6 OBTAINED BY COCRYSTALLIZATION
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 / positive regulation of fatty acid beta-oxidation / regulation of ketone metabolic process / cellular response to fructose stimulus / regulation of fatty acid metabolic process / negative regulation of cell growth involved in cardiac muscle cell development / negative regulation of appetite / negative regulation of hepatocyte apoptotic process ...positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / positive regulation of fatty acid beta-oxidation / regulation of ketone metabolic process / cellular response to fructose stimulus / regulation of fatty acid metabolic process / negative regulation of cell growth involved in cardiac muscle cell development / negative regulation of appetite / negative regulation of hepatocyte apoptotic process / positive regulation of fatty acid oxidation / lipoprotein metabolic process / behavioral response to nicotine / negative regulation of leukocyte cell-cell adhesion / negative regulation of glycolytic process / ubiquitin conjugating enzyme binding / mitogen-activated protein kinase kinase kinase binding / DNA-binding transcription activator activity / positive regulation of fatty acid metabolic process / NFAT protein binding / negative regulation of cholesterol storage / positive regulation of ATP biosynthetic process / nuclear steroid receptor activity / 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 / negative regulation of blood pressure / intracellular receptor signaling pathway / nitric oxide metabolic process / negative regulation of reactive oxygen species biosynthetic process / hormone-mediated signaling pathway / : / Regulation of lipid metabolism by PPARalpha / MDM2/MDM4 family protein binding / peroxisome proliferator activated receptor signaling pathway / response to nutrient / positive regulation of gluconeogenesis / negative regulation of cytokine production involved in inflammatory response / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / BMAL1:CLOCK,NPAS2 activates circadian expression / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / cellular response to starvation / gluconeogenesis / SUMOylation of intracellular receptors / circadian regulation of gene expression / wound healing / Heme signaling / negative regulation of transforming growth factor beta receptor signaling pathway / fatty acid metabolic process / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / response to insulin / Cytoprotection by HMOX1 / regulation of circadian rhythm / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription coactivator binding / nuclear receptor activity / : / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / gene expression / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / response to hypoxia / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / lipid binding / chromatin / positive regulation of DNA-templated transcription / protein-containing complex binding / 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-HW3 / Peroxisome proliferator-activated receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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

Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,3262
Polymers30,8561
Non-polymers4691
Water1,856103
1
A: Peroxisome proliferator-activated receptor alpha
hetero molecules

A: Peroxisome proliferator-activated receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6514
Polymers61,7122
Non-polymers9392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Unit cell
Length a, b, c (Å)44.599, 61.923, 53.148
Angle α, β, γ (deg.)90.000, 106.536, 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) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07869
#2: Chemical ChemComp-HW3 / (2S)-2-[[3-[[3-fluoranyl-4-(4-fluoranylphenoxy)phenyl]methylcarbamoyl]-4-methoxy-phenyl]methyl]butanoic acid


Mass: 469.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H25F2NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
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: Jul 29, 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: 1.66→50 Å / Num. obs: 60636 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 23.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.025 / Rrim(I) all: 0.037 / Net I/σ(I): 19.6
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1569 / CC1/2: 0.894 / Rpim(I) all: 0.294 / Rrim(I) all: 0.425 / % possible all: 97.8

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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: 1.66→42.75 Å / SU ML: 0.2117 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 28.684
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239 2943 4.85 %
Rwork0.2028 57693 -
obs0.2046 60636 94.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.86 Å2
Refinement stepCycle: LAST / Resolution: 1.66→42.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2085 0 34 103 2222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132246
X-RAY DIFFRACTIONf_angle_d1.29773041
X-RAY DIFFRACTIONf_chiral_restr0.0669342
X-RAY DIFFRACTIONf_plane_restr0.0098390
X-RAY DIFFRACTIONf_dihedral_angle_d13.2193864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.690.36781160.28042631X-RAY DIFFRACTION90.75
1.69-1.720.29941400.27232703X-RAY DIFFRACTION91.03
1.72-1.750.30671350.25742624X-RAY DIFFRACTION92.15
1.75-1.780.30651430.25392779X-RAY DIFFRACTION91.77
1.78-1.820.36491570.26492652X-RAY DIFFRACTION93.29
1.82-1.860.31481280.24442792X-RAY DIFFRACTION94.44
1.86-1.90.26841390.2542777X-RAY DIFFRACTION95.08
1.9-1.950.30461280.24672780X-RAY DIFFRACTION95.5
1.95-20.29811250.23442753X-RAY DIFFRACTION95.14
2-2.060.33691400.22822800X-RAY DIFFRACTION95.33
2.06-2.130.28341540.22722756X-RAY DIFFRACTION93.63
2.13-2.20.28181350.21932691X-RAY DIFFRACTION93.3
2.2-2.290.2321330.2132763X-RAY DIFFRACTION94.76
2.29-2.390.28571430.20522809X-RAY DIFFRACTION96.09
2.39-2.520.22011590.22132778X-RAY DIFFRACTION95.67
2.52-2.680.24411460.21732794X-RAY DIFFRACTION95.24
2.68-2.880.26951270.20782764X-RAY DIFFRACTION95.82
2.88-3.170.28321520.21832830X-RAY DIFFRACTION96.01
3.18-3.630.19251590.18512769X-RAY DIFFRACTION95.22
3.63-4.580.20981580.15942753X-RAY DIFFRACTION94.91
4.58-42.750.15741260.16712695X-RAY DIFFRACTION91.92

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