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- PDB-4f9m: Crystal structure of the PPARgamma-LBD complexed with a cercospor... -

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Basic information

Entry
Database: PDB / ID: 4f9m
TitleCrystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative modulator
Components
  • Peroxisome proliferator-activated receptor gamma
  • peptide from Nuclear receptor coactivator 1
KeywordsTRANSCRIPTION/TRANSCRIPTION REGULATOR / three-layered alpha-helical sandwich / transcription regulation / TRANSCRIPTION-TRANSCRIPTION REGULATOR complex
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 / prostaglandin receptor activity / : / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly ...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 / prostaglandin receptor activity / : / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of vascular endothelial cell proliferation / negative regulation of extracellular matrix assembly / negative regulation of connective tissue replacement involved in inflammatory response wound healing / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / arachidonate binding / positive regulation of adiponectin secretion / DNA binding domain binding / lipoprotein transport / negative regulation of cardiac muscle hypertrophy in response to stress / positive regulation of vascular associated smooth muscle cell apoptotic process / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K4 acetyltransferase activity / WW domain binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / positive regulation of fatty acid metabolic process / histone H3K56 acetyltransferase activity / STAT family protein binding / histone H3K23 acetyltransferase activity / response to lipid / histone H4K12 acetyltransferase activity / histone H4K16 acetyltransferase activity / histone H3K14 acetyltransferase activity / male mating behavior / histone H3K9 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / negative regulation of SMAD protein signal transduction / histone H3K122 acetyltransferase activity / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / hypothalamus development / histone H3K18 acetyltransferase activity / lipid homeostasis / histone H3K27 acetyltransferase activity / E-box binding / alpha-actinin binding / R-SMAD binding / negative regulation of vascular associated smooth muscle cell proliferation / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / cellular response to Thyroglobulin triiodothyronine / white fat cell differentiation / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / negative regulation of BMP signaling pathway / cell fate commitment / negative regulation of mitochondrial fission / negative regulation of osteoblast differentiation / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of fat cell differentiation / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / response to retinoic acid / estrous cycle / progesterone receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cell maturation / cellular response to hormone stimulus / Recycling of bile acids and salts / histone acetyltransferase / negative regulation of MAPK cascade / intracellular receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / lactation / hormone-mediated signaling pathway / estrogen receptor signaling pathway / positive regulation of adipose tissue development / : / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / epithelial cell differentiation / regulation of cellular response to insulin stimulus / response to nutrient / positive regulation of neuron differentiation / peptide binding / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / response to progesterone
Similarity search - Function
Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / 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 ...Nuclear receptor coactivator 1 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / 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 / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-FCM / Peroxisome proliferator-activated receptor gamma / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMatsui, Y. / Hanzawa, H.
CitationJournal: Eur.J.Med.Chem. / Year: 2012
Title: Synthesis and biological evaluation of novel (-)-cercosporamide derivatives as potent selective PPARg modulators
Authors: Furukawa, A. / Arita, T. / Fukuzaki, T. / Mori, M. / Honda, T. / Satoh, S. / Matsui, Y. / Wakabayashi, K. / Hayashi, S. / Nakamura, K. / Araki, K. / Kuroha, M. / Tanaka, J. / Wakimoto, S. / ...Authors: Furukawa, A. / Arita, T. / Fukuzaki, T. / Mori, M. / Honda, T. / Satoh, S. / Matsui, Y. / Wakabayashi, K. / Hayashi, S. / Nakamura, K. / Araki, K. / Kuroha, M. / Tanaka, J. / Wakimoto, S. / Suzuki, O. / Ohsumi, J.
History
DepositionMay 19, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 8, 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 Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7203
Polymers34,1892
Non-polymers5321
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-8 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.693, 54.167, 66.218
Angle α, β, γ (deg.)90.00, 91.38, 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 Nuclear receptor coactivator 1 / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal ...NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal carcinoma antigen NY-REN-52 / Steroid receptor coactivator 1 / SRC-1


Mass: 1776.072 Da / Num. of mol.: 1 / Fragment: LXXLL box, UNP residues 686-700 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788
#3: Chemical ChemComp-FCM / (9aS)-8-acetyl-N-[(2-ethyl-4-fluoronaphthalen-1-yl)methyl]-1,7-dihydroxy-3-methoxy-9a-methyl-9-oxo-9,9a-dihydrodibenzo[b,d]furan-4-carboxamide


Mass: 531.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H26FNO7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.03 Å3/Da / Density % sol: 39.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Sodium thiocyanate, Tris-HCl, 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: Oct 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 23474 / Num. obs: 23317 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 21.9 Å2 / Rsym value: 0.073 / Net I/σ(I): 18
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 2306 / Rsym value: 0.339 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CNX2000.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNX2000.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LMP

3lmp


Resolution: 1.9→19.37 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 923687.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflection
Rfree0.254 2168 10 %
Rwork0.228 --
obs-21575 99.4 %
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.6625 Å2 / ksol: 0.357278 e/Å3
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1-7.71 Å20 Å2-6.36 Å2
2---3.82 Å20 Å2
3----3.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2190 0 39 145 2374
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 335 9.3 %
Rwork0.268 3266 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3UNL.paramUNL.top

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