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- PDB-3b1m: Crystal structure of the PPARgamma-LBD complexed with a cercospor... -

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Basic information

Entry
Database: PDB / ID: 3b1m
TitleCrystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative modulator Cerco-A
Components
  • Peroxisome proliferator-activated receptor gamma
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / prostaglandin receptor activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to muscle activity ...Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / prostaglandin receptor activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to muscle activity / positive regulation of cholesterol transport / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of low-density lipoprotein receptor activity / cellular respiration / arachidonate binding / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / lncRNA binding / DNA binding domain binding / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / temperature homeostasis / STAT family protein binding / WW domain binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / LBD domain binding / response to starvation / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / E-box binding / intracellular glucose homeostasis / alpha-actinin binding / lipid homeostasis / fatty acid oxidation / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / response to dietary excess / negative regulation of blood vessel endothelial cell migration / negative regulation of macrophage derived foam cell differentiation / cellular response to low-density lipoprotein particle stimulus / negative regulation of lipid storage / white fat cell differentiation / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / cell fate commitment / negative regulation of MAPK cascade / BMP signaling pathway / adipose tissue development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / retinoic acid receptor signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / brown fat cell differentiation / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cell maturation / energy homeostasis / negative regulation of signaling receptor activity / digestion / positive regulation of gluconeogenesis / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / regulation of cellular response to insulin stimulus / negative regulation of angiogenesis / RNA splicing / respiratory electron transport chain / response to nutrient / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / Regulation of PTEN gene transcription / gluconeogenesis / transcription coregulator binding / mitochondrion organization / fatty acid metabolic process / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / positive regulation of apoptotic signaling pathway / negative regulation of smooth muscle cell proliferation / positive regulation of DNA-binding transcription factor activity / transcription coregulator activity / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / peptide binding / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / placenta development / regulation of circadian rhythm / PPARA activates gene expression
Similarity search - Function
PGC-1alpha, RNA recognition motif / PGC-1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X Receptor / RNA recognition motif ...PGC-1alpha, RNA recognition motif / PGC-1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / 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 / 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 / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-KRC / Peroxisome proliferator-activated receptor gamma / 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. / Hiroyuki, H.
CitationJournal: Biol.Pharm.Bull. / Year: 2011
Title: Pharmacology and in Vitro Profiling of a Novel Peroxisome Proliferator-Activated Receptor gamma Ligand, Cerco-A
Authors: Wakabayashi, K. / Hayashi, S. / Matsui, Y. / Matsumoto, T. / Furukawa, A. / Kuroha, M. / Tanaka, N. / Inaba, T. / Kanda, S. / Tanaka, J. / Okuyama, R. / Wakimoto, S. / Ogata, T. / Araki, K. / Ohsumi, J.
History
DepositionJul 5, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,9933
Polymers34,4802
Non-polymers5141
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-9 kcal/mol
Surface area13370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.946, 54.622, 66.782
Angle α, β, γ (deg.)90.00, 92.21, 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 / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / References: UniProt: P37231
#2: Protein/peptide 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
Fragment: peptide containing LXXLL box, UNP residues 136-154
Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2
#3: Chemical ChemComp-KRC / (9aS)-8-acetyl-N-[(2-ethylnaphthalen-1-yl)methyl]-1,7-dihydroxy-3-methoxy-9a-methyl-9-oxo-9,9a-dihydrodibenzo[b,d]furan-4-carboxamide


Mass: 513.538 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H27NO7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.06 Å3/Da / Density % sol: 40.25 %
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: Jun 28, 2005
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: 37106 / Num. obs: 36868 / % possible obs: 99.4 % / Biso Wilson estimate: 22.8 Å2 / Rsym value: 0.055
Reflection shellResolution: 1.6→1.66 Å / Mean I/σ(I) obs: 4.25 / Num. unique all: 3530 / Rsym value: 0.255 / % possible all: 96.2

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Processing

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

3lmp


Resolution: 1.6→19 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 867084.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.244 3682 10 %RANDOM
Rwork0.217 ---
obs0.217 36852 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.0583 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.72 Å20 Å2-1.57 Å2
2---1.26 Å20 Å2
3----2.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.6→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 38 278 2482
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.882
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.982.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 579 9.7 %
Rwork0.331 5402 -
obs-5402 97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3CRC.paramCRC.top

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