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- PDB-6ad9: Crystal Structure of PPARgamma Ligand Binding Domain in complex w... -

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Basic information

Entry
Database: PDB / ID: 6ad9
TitleCrystal Structure of PPARgamma Ligand Binding Domain in complex with dibenzooxepine derivative compound-9
Components
  • 12-mer peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
  • Peroxisome proliferator-activated receptor gamma
KeywordsNUCLEAR PROTEIN / PPARgamma Ligand Binding Domain Agonist
Function / homology
Function and homology information


Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration / lncRNA binding / digestion / temperature homeostasis / response to starvation / intracellular glucose homeostasis ...Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration / lncRNA binding / digestion / temperature homeostasis / response to starvation / intracellular glucose homeostasis / fatty acid oxidation / response to dietary excess / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Complex I biogenesis / adipose tissue development / Respiratory electron transport / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / brown fat cell differentiation / mitochondrial ATP synthesis coupled electron transport / energy homeostasis / transcription coregulator activity / mitochondrial respiratory chain complex I assembly / positive regulation of gluconeogenesis / respiratory electron transport chain / RNA splicing / negative regulation of smooth muscle cell proliferation / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / : / mitochondrion organization / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / gluconeogenesis / nuclear receptor binding / NADH dehydrogenase (ubiquinone) activity / regulation of circadian rhythm / transcription initiation at RNA polymerase II promoter / PPARA activates gene expression / positive regulation of DNA-binding transcription factor activity / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / mitochondrial membrane / aerobic respiration / PML body / chromatin DNA binding / mRNA processing / Regulation of RUNX2 expression and activity / Circadian Clock / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / DNA-binding transcription factor binding / protein-containing complex assembly / neuron apoptotic process / sequence-specific DNA binding / transcription coactivator activity / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / protein stabilization / mitochondrial inner membrane / ubiquitin protein ligase binding / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
PGC-1alpha, RNA recognition motif / PGC-1 / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / Retinoid X Receptor / Retinoid X Receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...PGC-1alpha, RNA recognition motif / PGC-1 / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / Retinoid X Receptor / Retinoid X Receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-KK4 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsTakahashi, Y. / Suzuki, M. / Yamamoto, K. / Saito, J.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Development of Dihydrodibenzooxepine Peroxisome Proliferator-Activated Receptor (PPAR) Gamma Ligands of a Novel Binding Mode as Anticancer Agents: Effective Mimicry of Chiral Structures by Olefinic E/ Z-Isomers.
Authors: Yamamoto, K. / Tamura, T. / Henmi, K. / Kuboyama, T. / Yanagisawa, A. / Matsubara, M. / Takahashi, Y. / Suzuki, M. / Saito, J.I. / Ueno, K. / Shuto, S.
History
DepositionJul 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor gamma
B: 12-mer peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4523
Polymers33,9592
Non-polymers4931
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-8 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.730, 54.338, 66.770
Angle α, β, γ (deg.)90.00, 108.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peroxisome proliferator-activated receptor gamma / PPAR-gamma / Nuclear receptor subfamily 1 group C member 3


Mass: 32693.824 Da / Num. of mol.: 1 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37231
#2: Protein/peptide 12-mer peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / PGC1-alpha


Mass: 1265.627 Da / Num. of mol.: 1 / Fragment: LXLL motif / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2
#3: Chemical ChemComp-KK4 / 3-[(1E)-1-{8-[(4-methyl-2-propyl-1H-benzimidazol-1-yl)methyl]dibenzo[b,e]oxepin-11(6H)-ylidene}ethyl]-1,2,4-oxadiazol-5(4H)-one


Mass: 492.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H28N4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.44 % / Mosaicity: 0.681 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 0.5M LiCl, 0.1M Tris-HCl pH 8.5, 28% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2009
RadiationProtocol: 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: 15196 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.17 / Χ2: 1.188 / Net I/σ(I): 4.5 / Num. measured all: 55697
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.2-2.283.70.61415041.0411100
2.28-2.373.70.52815051.041199.8
2.37-2.483.70.48215251.109199.7
2.48-2.613.70.41115011.128199.7
2.61-2.773.70.31115181.118199.9
2.77-2.993.70.2414961.126199.9
2.99-3.293.70.17515181.222199.8
3.29-3.763.70.11215281.33199.9
3.76-4.743.60.09215381.445199.9
4.74-503.50.07915631.318199

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.29 Å41.22 Å
Translation2.29 Å41.22 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREP10.2.12phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.22 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2399 762 5 %RANDOM
Rwork0.18451 ---
obs0.1874 14420 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.867 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å2-0.6 Å2
2--0.33 Å2-0 Å2
3---0.61 Å2
Refinement stepCycle: 1 / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 0 37 187 2341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192191
X-RAY DIFFRACTIONr_bond_other_d0.0020.022204
X-RAY DIFFRACTIONr_angle_refined_deg1.722.0192951
X-RAY DIFFRACTIONr_angle_other_deg1.02735082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8985261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22525.38591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92815425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.942158
X-RAY DIFFRACTIONr_chiral_restr0.1070.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022378
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02457
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0942.551056
X-RAY DIFFRACTIONr_mcbond_other2.0832.5491055
X-RAY DIFFRACTIONr_mcangle_it3.2733.7971313
X-RAY DIFFRACTIONr_mcangle_other3.2763.7981314
X-RAY DIFFRACTIONr_scbond_it2.7452.9121135
X-RAY DIFFRACTIONr_scbond_other2.7442.9121136
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4124.2141639
X-RAY DIFFRACTIONr_long_range_B_refined6.29420.7492688
X-RAY DIFFRACTIONr_long_range_B_other6.29320.7512689
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 51 -
Rwork0.266 1062 -
obs--99.55 %

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