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- PDB-7wgo: X-ray structure of human PPAR gamma ligand binding domain-bezafib... -

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Basic information

Entry
Database: PDB / ID: 7wgo
TitleX-ray structure of human PPAR gamma ligand binding domain-bezafibrate co-rystals obtained by co-crystallization
Components
  • 15-meric peptide from Nuclear receptor coactivator 1
  • Isoform 1 of Peroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / Nuclear receptor / Protein-ligand complex / PPAR
Function / homology
Function and homology information


labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / male mating behavior / hypothalamus development / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / progesterone receptor signaling pathway ...labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / male mating behavior / hypothalamus development / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / progesterone receptor signaling pathway / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / estrous cycle / nuclear retinoid X receptor binding / histone acetyltransferase activity / cellular response to hormone stimulus / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone acetyltransferase / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / estrogen receptor signaling pathway / lactation / : / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / cerebellum development / nuclear estrogen receptor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / male gonad development / : / response to estradiol / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / transcription regulator complex / Estrogen-dependent gene expression / transcription coactivator activity / protein dimerization activity / positive regulation of apoptotic process / chromatin binding / chromatin / positive regulation of DNA-templated transcription / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : ...Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
Chem-PEM / Isoform 1 of Peroxisome proliferator-activated receptor gamma / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.36 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: Isoform 1 of Peroxisome proliferator-activated receptor gamma
B: 15-meric peptide from Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0733
Polymers33,7112
Non-polymers3621
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-18 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.659, 64.946, 124.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Isoform 1 of Peroxisome proliferator-activated receptor gamma / PPAR-gamma


Mass: 31862.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG / Production host: Escherichia coli (E. coli) / References: UniProt: P37231-2
#2: Protein/peptide 15-meric peptide from Nuclear receptor coactivator 1


Mass: 1848.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-PEM / 2-[P-[2-P-CHLOROBENZAMIDO)ETHYL]PHENOXY]-2-METHYLPROPIONIC ACID


Mass: 361.819 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20ClNO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M Tris (pH 8.0), 1.1 M trisodium citrate

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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: 2.36→46.12 Å / Num. obs: 17210 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 46.74 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.016 / Rrim(I) all: 0.04 / Net I/σ(I): 28.7 / Num. measured all: 111695
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.36-2.456.30.3324.917410.9840.1430.36299.9
8.83-46.125.60.01576.739710.0070.01699.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.01 Å39.45 Å
Translation6.01 Å39.45 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: 1WM0

1wm0


Resolution: 2.36→39.449 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 26.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2253 1597 5.01 %
Rwork0.1949 30249 -
obs0.1964 17145 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.83 Å2 / Biso mean: 59.158 Å2 / Biso min: 29.18 Å2
Refinement stepCycle: final / Resolution: 2.36→39.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2324 0 44 8 2376
Biso mean--82.44 46.23 -
Num. residues----288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072390
X-RAY DIFFRACTIONf_angle_d1.0123221
X-RAY DIFFRACTIONf_chiral_restr0.05368
X-RAY DIFFRACTIONf_plane_restr0.004409
X-RAY DIFFRACTIONf_dihedral_angle_d18.8361469
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.36-2.43620.3711590.2778269299
2.4362-2.52320.27291460.24492751100
2.5232-2.62420.32241420.24752781100
2.6242-2.74360.30371580.24782720100
2.7436-2.88830.26541500.23622740100
2.8883-3.06920.2851350.23372771100
3.0692-3.3060.27411320.21942777100
3.306-3.63850.24791390.2022739100
3.6385-4.16450.1841460.17132765100
4.1645-5.24490.19271480.15842732100
5.2449-39.4490.16241420.17072781100

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