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- PDB-3ty0: Structure of PPARgamma ligand binding domain in complex with (R)-... -

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Basic information

Entry
Database: PDB / ID: 3ty0
TitleStructure of PPARgamma ligand binding domain in complex with (R)-5-(3-((3-(6-methoxybenzo[d]isoxazol-3-yl)-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)methyl)phenyl)-5-methyloxazolidine-2,4-dione
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION REGULATOR / nuclear receptor ligand binding domain
Function / homology
Function and homology information


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 / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonic acid binding ...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 / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonic acid binding / positive regulation of low-density lipoprotein receptor activity / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / positive regulation of vascular associated smooth muscle cell apoptotic process / macrophage derived foam cell differentiation / DNA binding domain binding / STAT family protein binding / 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 / negative regulation of cholesterol storage / E-box binding / alpha-actinin binding / negative regulation of blood vessel endothelial cell migration / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / positive regulation of cholesterol efflux / cellular response to low-density lipoprotein particle stimulus / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / long-chain fatty acid transport / retinoic acid receptor signaling pathway / positive regulation of DNA binding / cell fate commitment / BMP signaling pathway / nuclear retinoid X receptor binding / negative regulation of signaling receptor activity / regulation of cellular response to insulin stimulus / cell maturation / positive regulation of adipose tissue development / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / negative regulation of angiogenesis / response to nutrient / negative regulation of MAP kinase activity / fatty acid metabolic process / negative regulation of miRNA transcription / placenta development / Regulation of PTEN gene transcription / negative regulation of smooth muscle cell proliferation / transcription coregulator binding / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / lipid metabolic process / regulation of circadian rhythm / PPARA activates gene expression / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of blood pressure / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / activation of cysteine-type endopeptidase activity involved in apoptotic process / rhythmic process / nuclear receptor activity / : / positive regulation of DNA-binding transcription factor activity / glucose homeostasis / cellular response to hypoxia / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / nucleic acid binding / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / innate immune response / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding
Similarity search - Function
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 / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) ...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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-082 / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSoisson, S.M. / Meinke, P.M. / McKeever, B. / Liu, W.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Benzimidazolones: a new class of selective peroxisome proliferator-activated receptor gamma (PPAR-gamma) modulators.
Authors: Liu, W. / Lau, F. / Liu, K. / Wood, H.B. / Zhou, G. / Chen, Y. / Li, Y. / Akiyama, T.E. / Castriota, G. / Einstein, M. / Wang, C. / McCann, M.E. / Doebber, T.W. / Wu, M. / Chang, C.H. / ...Authors: Liu, W. / Lau, F. / Liu, K. / Wood, H.B. / Zhou, G. / Chen, Y. / Li, Y. / Akiyama, T.E. / Castriota, G. / Einstein, M. / Wang, C. / McCann, M.E. / Doebber, T.W. / Wu, M. / Chang, C.H. / McNamara, L. / McKeever, B. / Mosley, R.T. / Berger, J.P. / Meinke, P.T.
History
DepositionSep 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1564
Polymers63,1872
Non-polymers9692
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.510, 61.448, 119.914
Angle α, β, γ (deg.)90.000, 103.390, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 31593.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / References: UniProt: P37231
#2: Chemical ChemComp-082 / (5R)-5-(3-{[3-(6-methoxy-1,2-benzoxazol-3-yl)-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl]methyl}phenyl)-5-methyl-1,3-oxazolidine-2,4-dione


Mass: 484.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H20N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.62 Å3/Da / Density % sol: 53.12 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 63353 / Num. obs: 35537 / % possible obs: 79.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.045 / Χ2: 1.639 / Net I/σ(I): 16.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.071.40.3279011.03120.5
2.07-2.151.80.31718661.274142.4
2.15-2.252.20.25627311.385162.3
2.25-2.372.70.234161.46178.1
2.37-2.523.10.16239801.393190.1
2.52-2.713.40.11143361.288198.6
2.71-2.993.60.07643821.3531100
2.99-3.423.70.05144481.7441100
3.42-4.313.60.03544412.282199.9
4.31-503.50.02844311.906198

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.9.7refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
HKL-2000data scaling
BUSTER2.9.7refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.74 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.8992 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2728 1809 5.09 %RANDOM
Rwork0.2337 ---
all0.2356 63353 --
obs0.2356 35532 79.93 %-
Displacement parametersBiso max: 182.76 Å2 / Biso mean: 55.0355 Å2 / Biso min: 23.71 Å2
Baniso -1Baniso -2Baniso -3
1-3.0107 Å20 Å2-2.5983 Å2
2---10.6649 Å20 Å2
3---7.6541 Å2
Refine analyzeLuzzati coordinate error obs: 0.398 Å
Refinement stepCycle: LAST / Resolution: 2→37.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4440 0 72 91 4603
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1710SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes128HARMONIC8
X-RAY DIFFRACTIONt_gen_planes658HARMONIC8
X-RAY DIFFRACTIONt_it4600HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion598SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5464SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4600HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6216HARMONIC21.25
X-RAY DIFFRACTIONt_omega_torsion1.69
X-RAY DIFFRACTIONt_other_torsion44.04
LS refinement shellResolution: 2→2.06 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.3011 25 3.77 %
Rwork0.3076 638 -
all0.3073 663 -
obs--79.93 %

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