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- PDB-8dk4: Peroxisome proliferator-activated receptor gamma in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8dk4
TitlePeroxisome proliferator-activated receptor gamma in complex with VSP-51-2
Components
  • Peroxisome proliferator-activated receptor gamma
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
KeywordsSIGNALING PROTEIN / Peroxisome proliferator-activated receptor gamma / Modulator / VSP-51-2
Function / homology
Function and homology information


Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / prostaglandin receptor activity / regulation of cholesterol transporter 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 / response to muscle activity / negative regulation of extracellular matrix assembly / Activation of PPARGC1A (PGC-1alpha) by phosphorylation ...Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / prostaglandin receptor activity / regulation of cholesterol transporter 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 / response to muscle activity / negative regulation of extracellular matrix assembly / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration / negative regulation of vascular endothelial cell proliferation / lncRNA binding / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonate binding / positive regulation of low-density lipoprotein receptor activity / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / DNA binding domain binding / macrophage derived foam cell differentiation / STAT family protein binding / positive regulation of vascular associated smooth muscle cell apoptotic process / temperature homeostasis / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / LBD domain binding / negative regulation of type II interferon-mediated signaling pathway / response to starvation / negative regulation of cholesterol storage / E-box binding / intracellular glucose homeostasis / alpha-actinin binding / fatty acid oxidation / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / response to dietary excess / negative regulation of macrophage derived foam cell differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / white fat cell differentiation / negative regulation of BMP signaling pathway / negative regulation of mitochondrial fission / positive regulation of cholesterol efflux / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / retinoic acid receptor signaling pathway / cell fate commitment / BMP signaling pathway / adipose tissue development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / long-chain fatty acid transport / brown fat cell differentiation / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / energy homeostasis / cell maturation / negative regulation of signaling receptor activity / positive regulation of gluconeogenesis / digestion / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / respiratory electron transport chain / regulation of cellular response to insulin stimulus / negative regulation of angiogenesis / RNA splicing / response to nutrient / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / nuclear receptor coactivator activity / negative regulation of MAP kinase activity / mitochondrion organization / fatty acid metabolic process / Regulation of PTEN gene transcription / transcription coregulator binding / gluconeogenesis / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / negative regulation of smooth muscle cell proliferation / transcription coregulator activity / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / peptide binding / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / placenta development / regulation of circadian rhythm / PPARA activates gene expression / lipid metabolic process / PML body / chromatin DNA binding
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 / : / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...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 / : / 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
Similarity search - Domain/homology
Chem-SJ9 / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMa, L. / Zhou, X.E. / Suino-Powell, K. / Hou, N. / Zhou, Z. / Luo, J. / Xu, H.E. / Yi, W.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)21877020 China
National Science Foundation (NSF, China)22007020 China
CitationJournal: To Be Published
Title: Identification of VSP-51-2 as the Novel and Safe PPAR gamma Modulator: Structure-Based Design, Biological Validation and Crystal Analysis
Authors: Ma, L. / Zhou, X.E. / Suino-Powell, K. / Hou, N. / Zhou, Z. / Luo, J. / Xu, H.E. / Yi, W.
History
DepositionJul 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)33,1263
Polymers32,6892
Non-polymers4371
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-9 kcal/mol
Surface area13990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.200, 88.150, 122.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 31094.135 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 Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / PGC-1-alpha / PPAR-gamma coactivator 1-alpha / PPARGC-1-alpha / Ligand effect modulator 6


Mass: 1594.932 Da / Num. of mol.: 1 / Fragment: UNP residues 138-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARGC1A, LEM6, PGC1, PGC1A, PPARGC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBK2
#3: Chemical ChemComp-SJ9 / 5-(benzylcarbamoyl)-1-[(4-chloro-3-fluorophenyl)methyl]-1H-indole-2-carboxylic acid


Mass: 436.863 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H18ClFN2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M of trisodium citrate, pH 5.5, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→47.39 Å / Num. obs: 9684 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 66.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.043 / Rrim(I) all: 0.114 / Net I/σ(I): 6.3 / Num. measured all: 69144 / Scaling rejects: 143
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.727.31.421844911550.7780.5621.531.7100
9.01-47.395.70.03815552730.9970.0170.04110.299.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FM6

1fm6


Resolution: 2.6→44.184 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2554 662 6.87 %
Rwork0.2291 8980 -
obs0.2311 9642 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.72 Å2 / Biso mean: 82.0508 Å2 / Biso min: 43.94 Å2
Refinement stepCycle: final / Resolution: 2.6→44.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 31 4 2281
Biso mean--63.23 68.09 -
Num. residues----281
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.65310.3353360.363750899
2.6531-2.71080.4809330.3513517100
2.7108-2.77380.4064410.3359531100
2.7738-2.84320.363340.342251199
2.8432-2.920.3626440.343451799
2.92-3.00590.5374320.3089515100
3.0059-3.10290.3924320.3214537100
3.1029-3.21380.364260.2866530100
3.2138-3.34240.3737340.3024520100
3.3424-3.49450.2756390.2472544100
3.4945-3.67860.3325340.2571528100
3.6786-3.9090.2662310.2317521100
3.909-4.21060.2137440.1952533100
4.2106-4.63390.1993470.1928530100
4.6339-5.30350.2007550.1987524100
5.3035-6.67810.2431590.2192527100
6.6781-44.180.1914410.1654587100

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