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- PDB-7vwg: Human peroxisome proliferator-activated receptor (PPAR) delta lig... -

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Basic information

Entry
Database: PDB / ID: 7vwg
TitleHuman peroxisome proliferator-activated receptor (PPAR) delta ligand binding domain in complex with a synthetic alpha/delta dual agonist JKPL38
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 / adipose tissue development / NF-kappaB binding / positive regulation of fat cell differentiation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / response to glucose / 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 / nuclear receptor activity / glucose metabolic process / 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-820 / heptyl beta-D-glucopyranoside / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)64,4876
Polymers63,0552
Non-polymers1,4324
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-11 kcal/mol
Surface area23810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.500, 94.314, 96.247
Angle α, β, γ (deg.)90.000, 97.372, 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: 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
IdentifierTypeProgram
heptyl-b-D-GlucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-820 / (2S)-2-[[4-propoxy-3-[[[4-(trifluoromethyl)phenyl]carbonylamino]methyl]phenyl]methyl]butanoic acid


Mass: 437.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H26F3NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 56.38 %
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: 2.2→50 Å / Num. obs: 66164 / % possible obs: 99.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 33.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.039 / Rrim(I) all: 0.073 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3011 / CC1/2: 0.894 / Rpim(I) all: 0.277 / Rrim(I) all: 0.511 / % possible all: 99.9

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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: 2.2→42.58 Å / SU ML: 0.2787 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 26.6802
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2316 3279 4.96 %
Rwork0.2002 62885 -
obs0.2017 66164 94.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.69 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4161 0 100 78 4339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214352
X-RAY DIFFRACTIONf_angle_d0.52915879
X-RAY DIFFRACTIONf_chiral_restr0.0372672
X-RAY DIFFRACTIONf_plane_restr0.0039731
X-RAY DIFFRACTIONf_dihedral_angle_d13.37391640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.31831500.26612610X-RAY DIFFRACTION93.88
2.23-2.270.26121390.26952795X-RAY DIFFRACTION97.12
2.27-2.30.3711730.27872840X-RAY DIFFRACTION97.04
2.3-2.340.29961390.2592781X-RAY DIFFRACTION96.66
2.34-2.390.30281220.24732779X-RAY DIFFRACTION97.15
2.39-2.430.30581480.26022836X-RAY DIFFRACTION97.17
2.43-2.480.27761180.25532872X-RAY DIFFRACTION97.24
2.48-2.540.3611530.2422776X-RAY DIFFRACTION96.44
2.54-2.60.32491520.2412783X-RAY DIFFRACTION96.83
2.6-2.660.24941620.24032764X-RAY DIFFRACTION96.38
2.66-2.730.27421510.23752746X-RAY DIFFRACTION96.44
2.73-2.810.25191410.23482863X-RAY DIFFRACTION96.87
2.81-2.90.27231580.22512705X-RAY DIFFRACTION95.78
2.9-3.010.26781340.22262826X-RAY DIFFRACTION95.09
3.01-3.130.26281440.23432590X-RAY DIFFRACTION92.52
3.13-3.270.22321120.22652772X-RAY DIFFRACTION93.18
3.27-3.440.27631160.2132734X-RAY DIFFRACTION94.5
3.44-3.660.21161550.19062707X-RAY DIFFRACTION93.59
3.66-3.940.22671460.17552656X-RAY DIFFRACTION91.78
3.94-4.340.17881540.16332642X-RAY DIFFRACTION91.94
4.34-4.960.19781440.15132600X-RAY DIFFRACTION90.17
4.96-6.250.18621430.17382570X-RAY DIFFRACTION89.69
6.25-42.580.14111250.13742638X-RAY DIFFRACTION91.07

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