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- PDB-5two: Peroxisome proliferator-activated receptor gamma ligand binding d... -

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Basic information

Entry
Database: PDB / ID: 5two
TitlePeroxisome proliferator-activated receptor gamma ligand binding domain in complex with a novel selectively PPAR gamma-modulating ligand VSP-51
Components
  • PRO-SER-LEU-LEU-LYS-LYS-LEU-LEU-LEU-ALA-PRO
  • Peroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / Peroxisome proliferator-activated receptor gamma / lignad binding domain / selective PPAR gamma ligand / VSP-51 / DNA BINDING PROTEIN
Function / homology
Function and homology information


Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / fatty acid oxidation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / prostaglandin receptor activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / cellular respiration / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly ...Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / fatty acid oxidation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / prostaglandin receptor activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / cellular respiration / 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 / white fat cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / DNA binding domain binding / negative regulation of cardiac muscle hypertrophy in response to stress / response to muscle activity / positive regulation of lipid metabolic process / response to starvation / STAT family protein binding / positive regulation of fatty acid metabolic process / WW domain binding / negative regulation of type II interferon-mediated signaling pathway / adipose tissue development / energy homeostasis / LBD domain binding / negative regulation of cholesterol storage / temperature homeostasis / response to lipid / positive regulation of lipoprotein transport / cell fate commitment / lipid homeostasis / negative regulation of SMAD protein signal transduction / lncRNA binding / cell maturation / E-box binding / R-SMAD binding / negative regulation of BMP signaling pathway / brown fat cell differentiation / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of vascular associated smooth muscle cell proliferation / alpha-actinin binding / negative regulation of macrophage derived foam cell differentiation / BMP signaling pathway / negative regulation of lipid storage / positive regulation of cholesterol efflux / positive regulation of fat cell differentiation / cellular response to low-density lipoprotein particle stimulus / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / fat cell differentiation / long-chain fatty acid transport / negative regulation of mitochondrial fission / negative regulation of osteoblast differentiation / placenta development / nuclear retinoid X receptor binding / retinoic acid receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / digestion / positive regulation of gluconeogenesis / hormone-mediated signaling pathway / intracellular receptor signaling pathway / negative regulation of MAPK cascade / peroxisome proliferator activated receptor signaling pathway / positive regulation of adipose tissue development / gluconeogenesis / peptide binding / negative regulation of angiogenesis / epithelial cell differentiation / response to nutrient / regulation of cellular response to insulin stimulus / positive regulation of apoptotic signaling pathway / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / SUMOylation of transcription cofactors / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / negative regulation of miRNA transcription / fatty acid metabolic process / intracellular glucose homeostasis / RNA splicing / negative regulation of transforming growth factor beta receptor signaling pathway / nuclear receptor binding / Regulation of PTEN gene transcription / transcription coregulator binding / negative regulation of smooth muscle cell proliferation / mitochondrion organization / SUMOylation of intracellular receptors / circadian regulation of gene expression / respiratory electron transport chain / RNA polymerase II transcription regulator complex / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / negative regulation of inflammatory response / transcription initiation at RNA polymerase II promoter / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway
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 / 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 / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7MV / Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.927 Å
AuthorsYi, W. / Shi, J. / Zhao, G. / Zhou, X.E. / Suino-Powell, K. / Melcher, K. / Xu, H.E.
Funding support China, 2items
OrganizationGrant numberCountry
Youth Innovation Promotion Association CAS, the Shanghai Municipal Natural Science Foundation15ZR1447800 China
the Chinese Postdoctoral Science Foundation2014M560363 China
CitationJournal: Sci Rep / Year: 2017
Title: Identification of a novel selective PPAR gamma ligand with a unique binding mode and improved therapeutic profile in vitro.
Authors: Yi, W. / Shi, J. / Zhao, G. / Zhou, X.E. / Suino-Powell, K. / Melcher, K. / Xu, H.E.
History
DepositionNov 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisome proliferator-activated receptor gamma
B: PRO-SER-LEU-LEU-LYS-LYS-LEU-LEU-LEU-ALA-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0823
Polymers32,6892
Non-polymers3931
Water2,234124
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-9 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.893, 88.504, 122.163
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-695-

HOH

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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: lignad 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 PRO-SER-LEU-LEU-LYS-LYS-LEU-LEU-LEU-ALA-PRO


Mass: 1594.932 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others) / References: UniProt: Q9UBK2*PLUS
#3: Chemical ChemComp-7MV / N-benzyl-1-[(4-chloro-3-fluorophenyl)methyl]-1H-indole-5-carboxamide


Mass: 392.853 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H18ClFN2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 0.1 M of tri-sodium citrate (pH 5.5), 20% w/v PEG 3350
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 23586 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.031 / Net I/σ(I): 26.6
Reflection shellResolution: 1.92→1.95 Å / Rmerge(I) obs: 0.792 / Rrim(I) all: 0.317

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U9Q

3u9q


Resolution: 1.927→37.672 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2365 1584 6.72 %
Rwork0.2087 --
obs0.2107 23586 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.927→37.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 28 124 2395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082312
X-RAY DIFFRACTIONf_angle_d1.1433116
X-RAY DIFFRACTIONf_dihedral_angle_d11.737880
X-RAY DIFFRACTIONf_chiral_restr0.039361
X-RAY DIFFRACTIONf_plane_restr0.005390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9272-1.96650.3525710.30171221X-RAY DIFFRACTION93
1.9665-2.00930.3812920.29171267X-RAY DIFFRACTION100
2.0093-2.0560.27850.25261275X-RAY DIFFRACTION100
2.056-2.10740.2553870.22791317X-RAY DIFFRACTION100
2.1074-2.16440.2475910.24661259X-RAY DIFFRACTION100
2.1644-2.22810.2793800.23451301X-RAY DIFFRACTION100
2.2281-2.30.28651020.23221290X-RAY DIFFRACTION100
2.3-2.38220.298900.2241292X-RAY DIFFRACTION100
2.3822-2.47750.2548910.23081286X-RAY DIFFRACTION100
2.4775-2.59030.26121010.23731288X-RAY DIFFRACTION100
2.5903-2.72680.2513980.23311278X-RAY DIFFRACTION100
2.7268-2.89760.27031110.21721291X-RAY DIFFRACTION100
2.8976-3.12120.2835850.2351299X-RAY DIFFRACTION100
3.1212-3.43510.23291170.22551289X-RAY DIFFRACTION100
3.4351-3.93170.2219880.18471320X-RAY DIFFRACTION100
3.9317-4.95180.1928900.16681343X-RAY DIFFRACTION100
4.9518-37.6790.18131050.17731386X-RAY DIFFRACTION99

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