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- PDB-3v9v: Crystal structure of the PPARgamma-LBD complexed with a cercospor... -

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Basic information

Entry
Database: PDB / ID: 3v9v
TitleCrystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative modulator
Components
  • Peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
  • Peroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION/TRANSCRIPTION REGULATOR / three-layered alpha-helical sandwich / transcription regulation / TRANSCRIPTION-TRANSCRIPTION REGULATOR complex
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-21L / 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 / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMatsui, Y. / Hanzawa, H.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Substituents at the naphthalene C3 position of (-)-Cercosporamide derivatives significantly affect the maximal efficacy as PPAR(gamma) partial agonists
Authors: Furukawa, A. / Arita, T. / Fukuzaki, T. / Satoh, S. / Mori, M. / Honda, T. / Matsui, Y. / Wakabayashi, K. / Hayashi, S. / Araki, K. / Ohsumi, J.
History
DepositionDec 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0523
Polymers34,4802
Non-polymers5721
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-9 kcal/mol
Surface area12990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.910, 54.516, 66.543
Angle α, β, γ (deg.)90.00, 91.89, 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: 32412.576 Da / Num. of mol.: 1 / Fragment: ligand binding domain, UNP residues 234-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli (E. coli) / References: UniProt: P37231
#2: Protein/peptide Peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / PGC-1-alpha / PPAR-gamma coactivator 1-alpha / PPARGC-1-alpha / Ligand effect modulator 6


Mass: 2067.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2
#3: Chemical ChemComp-21L / methyl 3-{4-[({[(9aS)-8-acetyl-1,7-dihydroxy-3-methoxy-9a-methyl-9-oxo-9,9a-dihydrodibenzo[b,d]furan-4-yl]carbonyl}amino)methyl]naphthalen-2-yl}propanoate


Mass: 571.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H29NO9
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.05 Å3/Da / Density % sol: 39.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, sodium thiocyanate, Tris-hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 36814 / Num. obs: 36676 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.066
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.3 % / Num. unique all: 3644 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CNSrefinement
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LMP

3lmp


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.91 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24403 3667 10 %RANDOM
Rwork0.22415 ---
obs0.22618 32975 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.196 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å2-0.05 Å2
2---0.18 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2150 0 42 168 2360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0222232
X-RAY DIFFRACTIONr_bond_other_d0.0010.021520
X-RAY DIFFRACTIONr_angle_refined_deg1.0032.0233015
X-RAY DIFFRACTIONr_angle_other_deg0.77533745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2215266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81725.37693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56815427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.739158
X-RAY DIFFRACTIONr_chiral_restr0.0420.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022435
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02415
X-RAY DIFFRACTIONr_mcbond_it0.351.51344
X-RAY DIFFRACTIONr_mcbond_other0.041.5539
X-RAY DIFFRACTIONr_mcangle_it0.67822175
X-RAY DIFFRACTIONr_scbond_it0.9393888
X-RAY DIFFRACTIONr_scangle_it1.5784.5840
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 241 -
Rwork0.258 2381 -
obs--97.15 %

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