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- PDB-7wgn: X-ray structure of human PPAR delta ligand binding domain-pemafib... -

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Basic information

Entry
Database: PDB / ID: 7wgn
TitleX-ray structure of human PPAR delta ligand binding domain-pemafibrate co-crystals obtained by co-crystallization
ComponentsPeroxisome proliferator-activated receptor delta
KeywordsTRANSCRIPTION / Nuclear receptor / Protein-ligand complex / PPAR
Function / homology
Function and homology information


fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process ...fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process / negative regulation of myoblast differentiation / Carnitine metabolism / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / nuclear steroid receptor activity / fatty acid beta-oxidation / positive regulation of fatty acid metabolic process / cell-substrate adhesion / negative regulation of cholesterol storage / cellular response to nutrient levels / decidualization / keratinocyte proliferation / positive regulation of fat cell differentiation / fatty acid transport / adipose tissue development / energy homeostasis / embryo implantation / cholesterol metabolic process / hormone-mediated signaling pathway / fatty acid metabolic process / negative regulation of miRNA transcription / phosphatidylinositol 3-kinase/protein kinase B signal transduction / generation of precursor metabolites and energy / apoptotic signaling pathway / wound healing / lipid metabolic process / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / Nuclear Receptor transcription pathway / glucose metabolic process / nuclear receptor activity / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / cellular response to hypoxia / DNA-binding transcription factor binding / cell population proliferation / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / 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 / 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 ...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 / 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
Similarity search - Domain/homology
Chem-P7F / Peroxisome proliferator-activated receptor delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.813 Å
AuthorsKamata, S. / Honda, A. / Akahane, M. / Machida, Y. / Uchii, K. / Shiiyama, Y. / Masuda, R. / Oyama, T. / Ishii, I.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K16359 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101071 Japan
CitationJournal: Int J Mol Sci / Year: 2022
Title: Functional and Structural Insights into Human PPAR alpha / delta / gamma Subtype Selectivity of Bezafibrate, Fenofibric Acid, and Pemafibrate.
Authors: Honda, A. / Kamata, S. / Akahane, M. / Machida, Y. / Uchii, K. / Shiiyama, Y. / Habu, Y. / Miyawaki, S. / Kaneko, C. / Oyama, T. / Ishii, I.
History
DepositionDec 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3113
Polymers31,5281
Non-polymers7832
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint1 kcal/mol
Surface area12650 Å2
Unit cell
Length a, b, c (Å)37.772, 92.662, 96.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARD, NR1C2, PPARB / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q03181
#2: Chemical ChemComp-P7F / (2~{R})-2-[3-[[1,3-benzoxazol-2-yl-[3-(4-methoxyphenoxy)propyl]amino]methyl]phenoxy]butanoic acid / Pemafibrate


Mass: 490.548 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H30N2O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: agonist*YM
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.05 M Bis-tis propane (pH 8.5), 14% PEG8000, 0.2 M KCl, 6% propanediol, 0.001 M EDTA, 0.001 M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 20, 2021 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→48.38 Å / Num. obs: 31614 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 28.15 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.014 / Rrim(I) all: 0.035 / Net I/σ(I): 29 / Num. measured all: 207167
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.81-1.856.60.3894.417920.9730.1630.42397.4
9.06-48.385.80.01788.731410.0070.01999.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.02 Å48.38 Å
Translation4.02 Å48.38 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.21data scaling
PHASER2.7.16phasing
PHENIX1.11.1-2575-000refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GZ9

3gz9


Resolution: 1.813→37.772 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 26.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2548 2917 4.92 %
Rwork0.2261 56322 -
obs0.2275 31538 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.75 Å2 / Biso mean: 34.6528 Å2 / Biso min: 16.01 Å2
Refinement stepCycle: final / Resolution: 1.813→37.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 113 58 2272
Biso mean--40.27 33.48 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022232
X-RAY DIFFRACTIONf_angle_d0.5893015
X-RAY DIFFRACTIONf_chiral_restr0.035341
X-RAY DIFFRACTIONf_plane_restr0.002376
X-RAY DIFFRACTIONf_dihedral_angle_d14.021333
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.813-1.84270.28621370.2791255896
1.8427-1.87440.30511420.26692698100
1.8744-1.90850.2871480.27252679100
1.9085-1.94520.32821310.2896268999
1.9452-1.98490.34441200.27422739100
1.9849-2.02810.28311410.28012645100
2.0281-2.07530.35511220.26732730100
2.0753-2.12720.28531530.25922671100
2.1272-2.18470.27121630.26612637100
2.1847-2.24890.3261310.25782711100
2.2489-2.32150.35661180.25632707100
2.3215-2.40450.21031530.2503265099
2.4045-2.50070.2591180.23672751100
2.5007-2.61450.27191630.25352631100
2.6145-2.75230.26971250.25722703100
2.7523-2.92470.27641760.23952676100
2.9247-3.15040.2771610.23242678100
3.1504-3.46730.27521420.22782684100
3.4673-3.96850.22431300.20212670100
3.9685-4.99810.20331230.17862705100
4.9981-37.7720.18341200.18662710100

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