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- PDB-4y29: Identification of a novel PPARg ligand that regulates metabolism -

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Basic information

Entry
Database: PDB / ID: 4y29
TitleIdentification of a novel PPARg ligand that regulates metabolism
Components
  • Peptide from Nuclear receptor coactivator 1
  • Peroxisome proliferator-activated receptor gamma
KeywordsDNA BINDING PROTEIN/TRANSCRIPTION / AF-2 helix / ligand binding pocket / three-layer helical sandwich / transcription regulator PPARg / NR1C3 / Peroxisome proliferator-activated receptor gamma / NHR / nuclear receptor / coactivator / Transcription factor / DNA BINDING PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / 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 / beige fat cell differentiation ...labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / 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 / beige fat cell differentiation / negative regulation of vascular endothelial cell proliferation / positive regulation of cholesterol transport / negative regulation of cellular response to transforming growth factor beta stimulus / arachidonate binding / positive regulation of adiponectin secretion / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / white fat cell differentiation / DNA binding domain binding / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of cardiac muscle hypertrophy in response to stress / positive regulation of lipid metabolic process / STAT family protein binding / positive regulation of fatty acid metabolic process / WW domain binding / hypothalamus development / negative regulation of type II interferon-mediated signaling pathway / male mating behavior / LBD domain binding / negative regulation of cholesterol storage / lipid homeostasis / response to lipid / positive regulation of lipoprotein transport / negative regulation of SMAD protein signal transduction / E-box binding / progesterone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / R-SMAD binding / Synthesis of bile acids and bile salts / monocyte differentiation / brown fat cell differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of BMP signaling pathway / cell fate commitment / negative regulation of vascular associated smooth muscle cell proliferation / alpha-actinin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / BMP signaling pathway / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of cholesterol efflux / Endogenous sterols / positive regulation of fat cell differentiation / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / cellular response to low-density lipoprotein particle stimulus / response to retinoic acid / fat cell differentiation / long-chain fatty acid transport / protein-lysine-acetyltransferase activity / negative regulation of mitochondrial fission / negative regulation of osteoblast differentiation / nuclear retinoid X receptor binding / estrous cycle / cell maturation / retinoic acid receptor signaling pathway / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone acetyltransferase / lactation / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / estrogen receptor signaling pathway / cellular response to hormone stimulus / intracellular receptor signaling pathway / negative regulation of MAPK cascade / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / Regulation of lipid metabolism by PPARalpha / response to progesterone / cerebellum development / positive regulation of adipose tissue development / peptide binding / positive regulation of neuron differentiation / epithelial cell differentiation / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian expression / regulation of cellular response to insulin stimulus / placenta development / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / negative regulation of miRNA transcription / fatty acid metabolic process / negative regulation of angiogenesis / positive regulation of apoptotic signaling pathway / nuclear estrogen receptor binding / nuclear receptor binding / hippocampus development / Regulation of PTEN gene transcription / transcription coregulator binding / negative regulation of smooth muscle cell proliferation
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-CTI / Peroxisome proliferator-activated receptor gamma / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsWang, R. / Li, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31270776 China
CitationJournal: Sci Rep / Year: 2015
Title: Selective targeting of PPAR gamma by the natural product chelerythrine with a unique binding mode and improved antidiabetic potency.
Authors: Zheng, W.L. / Qiu, L. / Wang, R. / Feng, X.H. / Han, Y.P. / Zhu, Y.L. / Chen, D.Z. / Liu, Y.J. / Jin, L.H. / Li, Y.
History
DepositionFeb 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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: Peptide from Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2263
Polymers31,8782
Non-polymers3481
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-9 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.624, 54.514, 66.402
Angle α, β, γ (deg.)90.000, 107.070, 90.000
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: 30704.734 Da / Num. of mol.: 1 / Fragment: UNP residues 236-504
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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: 1173.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788
#3: Chemical ChemComp-CTI / 1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium / chelerythrine


Mass: 348.372 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C21H18NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium thiocyanate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.005 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 21090 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.068 / Χ2: 1.198 / Net I/av σ(I): 24.83 / Net I/σ(I): 11.6 / Num. measured all: 110768
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.98-2.015.20.35610510.893100
2.01-2.055.20.31710280.934100
2.05-2.095.20.26310730.96100
2.09-2.135.30.22310391.024100
2.13-2.185.30.21610590.996100
2.18-2.235.30.18510181.027100
2.23-2.295.30.1610581.148100
2.29-2.355.20.14510561.1100
2.35-2.425.30.13110341.127100
2.42-2.495.30.11610611.176100
2.49-2.585.30.10510571.156100
2.58-2.695.30.09410481.232100
2.69-2.815.30.0810411.226100
2.81-2.965.30.06810601.223100
2.96-3.145.30.0610571.335100
3.14-3.395.30.05310621.701100
3.39-3.735.30.04410531.65299.9
3.73-4.265.30.03310671.36199.9
4.26-5.375.30.0310691.28699.3
5.37-5050.02710991.38299.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SCALEPACKdata reduction
PHASER2.5.1phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U9Q

3u9q


Resolution: 1.98→41.36 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2127 / WRfactor Rwork: 0.1718 / FOM work R set: 0.8657 / SU B: 3.434 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1703 / SU Rfree: 0.1522 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 1068 5.1 %RANDOM
Rwork0.177 ---
obs0.1791 19842 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 82.83 Å2 / Biso mean: 26.6 Å2 / Biso min: 6.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.02 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.98→41.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 26 197 2358
Biso mean--39 31.5 -
Num. residues----267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222197
X-RAY DIFFRACTIONr_angle_refined_deg2.0692.0112962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8535264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01925.53294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55415429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.788158
X-RAY DIFFRACTIONr_chiral_restr0.1480.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211579
X-RAY DIFFRACTIONr_mcbond_it1.5361.51330
X-RAY DIFFRACTIONr_mcangle_it2.7722152
X-RAY DIFFRACTIONr_scbond_it4.0563867
X-RAY DIFFRACTIONr_scangle_it6.774.5810
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 82 -
Rwork0.216 1448 -
all-1530 -
obs--100 %

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