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- PDB-7vwh: human peroxisome proliferator-activated receptor (PPAR) delta lig... -

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Basic information

Entry
Database: PDB / ID: 7vwh
Titlehuman peroxisome proliferator-activated receptor (PPAR) delta ligand binding domain in complex with a synthetic agonist JKPL39
ComponentsPeroxisome proliferator-activated receptor delta
KeywordsTRANSCRIPTION / NUCLEAR RECEPTOR / PROTEIN-LIGAND COMPLEX / PPAR
Function / homology
Function and homology information


keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / fat cell proliferation / positive regulation of epidermis development / axon ensheathment / positive regulation of fat cell proliferation / regulation of skeletal muscle satellite cell proliferation / D-glucose transmembrane transport / negative regulation of smooth muscle cell migration ...keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / fat cell proliferation / positive regulation of epidermis development / axon ensheathment / positive regulation of fat cell proliferation / regulation of skeletal muscle satellite cell proliferation / D-glucose transmembrane transport / negative regulation of smooth muscle cell migration / proteoglycan metabolic process / fatty acid catabolic process / negative regulation of collagen biosynthetic process / positive regulation of myoblast proliferation / 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 / fatty acid beta-oxidation / cell-substrate adhesion / negative regulation of cholesterol storage / decidualization / nuclear steroid receptor activity / keratinocyte proliferation / NF-kappaB binding / adipose tissue development / positive regulation of fat cell differentiation / response to glucose / positive regulation of insulin secretion involved in cellular response to glucose stimulus / fatty acid transport / cellular response to nutrient levels / cholesterol metabolic process / energy homeostasis / intracellular receptor signaling pathway / hormone-mediated signaling pathway / embryo implantation / negative regulation of miRNA transcription / response to activity / generation of precursor metabolites and energy / apoptotic signaling pathway / negative regulation of smooth muscle cell proliferation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / wound healing / fatty acid metabolic process / negative regulation of cell growth / Nuclear Receptor transcription pathway / lipid metabolic process / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription coactivator binding / vasodilation / glucose metabolic process / nuclear receptor activity / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / heart development / cellular response to lipopolysaccharide / cellular response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / 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 / : / 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, beta / 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-82K / heptyl beta-D-glucopyranoside / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOyama, T. / Miyachi, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJTM20NM Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Crystal structures of the ligand-binding domain of human peroxisome proliferator-activated receptor delta in complexes with phenylpropanoic acid derivatives and a pyridine carboxylic acid derivative.
Authors: Oyama, T. / Takiguchi, K. / Miyachi, H.
History
DepositionNov 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2022Provider: 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor delta
B: Peroxisome proliferator-activated receptor delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5716
Polymers63,0552
Non-polymers1,5164
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-10 kcal/mol
Surface area23820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.588, 94.139, 96.184
Angle α, β, γ (deg.)90.000, 96.635, 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 delta / PPAR-delta / NUCI / Nuclear hormone receptor 1 / NUC1 / Nuclear receptor subfamily 1 group C member ...PPAR-delta / NUCI / Nuclear hormone receptor 1 / NUC1 / Nuclear receptor subfamily 1 group C member 2 / Peroxisome proliferator-activated receptor beta / PPAR-beta


Mass: 31527.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARD, NR1C2, PPARB / Production host: Escherichia coli (E. coli) / References: UniProt: Q03181
#2: Chemical ChemComp-82K / (2S)-2-[[4-hexoxy-3-[[[4-(trifluoromethyl)phenyl]carbonylamino]methyl]phenyl]methyl]butanoic acid


Mass: 479.532 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H32F3NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-B7G / heptyl beta-D-glucopyranoside / HEPTYL-BETA-D-GLUCOPYRANOSIDE / heptyl beta-D-glucoside / heptyl D-glucoside / heptyl glucoside


Type: D-saccharide / Mass: 278.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H26O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
heptyl-b-D-GlucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.82 Å3/Da / Density % sol: 56.43 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 14% PEG8000, 200MM KCL, 40MM BISTRIS ETHANE, 6% PROPANEDIOL, 0.5% N-HEPTYL-BETA-D-GLUCOPYRANOSIDE, 1MM EDTA, 1MM CACL2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 8, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 75036 / % possible obs: 98.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 32.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.034 / Rrim(I) all: 0.062 / Net I/σ(I): 14.3
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 3 / Num. unique obs: 3313 / CC1/2: 0.882 / Rpim(I) all: 0.276 / Rrim(I) all: 0.513 / % possible all: 99.7

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Processing

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

2znp


Resolution: 2.1→42.6 Å / SU ML: 0.2399 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 27.9209
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2397 3578 4.77 %
Rwork0.2052 71458 -
obs0.207 75036 93.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4169 0 106 68 4343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00484366
X-RAY DIFFRACTIONf_angle_d0.72685896
X-RAY DIFFRACTIONf_chiral_restr0.0415673
X-RAY DIFFRACTIONf_plane_restr0.0053733
X-RAY DIFFRACTIONf_dihedral_angle_d14.43931649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.33851120.2742788X-RAY DIFFRACTION94.74
2.13-2.160.29721360.26282741X-RAY DIFFRACTION93.26
2.16-2.190.33181350.25952835X-RAY DIFFRACTION93.84
2.19-2.220.28481340.2552724X-RAY DIFFRACTION92.55
2.22-2.250.31531420.262730X-RAY DIFFRACTION94.47
2.25-2.290.33131280.25342849X-RAY DIFFRACTION95.88
2.29-2.330.29851470.24832837X-RAY DIFFRACTION94.97
2.33-2.370.30351320.23252793X-RAY DIFFRACTION95.81
2.37-2.420.32681470.23412842X-RAY DIFFRACTION96.67
2.42-2.470.2721280.23772893X-RAY DIFFRACTION96.39
2.47-2.520.27661220.23682866X-RAY DIFFRACTION96.11
2.52-2.580.28711370.23252789X-RAY DIFFRACTION96.12
2.58-2.650.26851730.23262843X-RAY DIFFRACTION95.38
2.65-2.720.28381210.22972775X-RAY DIFFRACTION95.83
2.72-2.80.28851580.22272833X-RAY DIFFRACTION95.19
2.8-2.890.27681390.22512756X-RAY DIFFRACTION94.36
2.89-2.990.211220.2442819X-RAY DIFFRACTION94.05
2.99-3.110.3091470.24882688X-RAY DIFFRACTION91.33
3.11-3.250.26991580.23792692X-RAY DIFFRACTION92.29
3.25-3.420.27921950.20992576X-RAY DIFFRACTION89.85
3.42-3.640.21251790.20692681X-RAY DIFFRACTION91.73
3.64-3.920.21841270.19482655X-RAY DIFFRACTION89.77
3.92-4.310.19221160.16652614X-RAY DIFFRACTION88.61
4.31-4.930.1851330.15062628X-RAY DIFFRACTION88.44
4.94-6.210.2366820.18132618X-RAY DIFFRACTION88.03
6.22-42.60.11911280.14412593X-RAY DIFFRACTION87.69

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