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- PDB-3po9: Crystal structure of PPARgamma ligand binding domain in complex w... -

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Basic information

Entry
Database: PDB / ID: 3po9
TitleCrystal structure of PPARgamma ligand binding domain in complex with tripropyltin
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / ligand binding domain
Function / homology
Function and homology information


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 ...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 / negative regulation of cardiac muscle hypertrophy in response to stress / DNA binding domain binding / lipoprotein transport / positive regulation of vascular associated smooth muscle cell apoptotic process / WW domain binding / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / lipid homeostasis / E-box binding / alpha-actinin binding / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / 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 / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / cell fate commitment / negative regulation of osteoblast differentiation / positive regulation of fat cell differentiation / negative regulation of MAPK cascade / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cell maturation / intracellular receptor signaling pathway / positive regulation of adipose tissue development / hormone-mediated signaling pathway / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / response to nutrient / negative regulation of miRNA transcription / peptide binding / negative regulation of angiogenesis / transcription coregulator binding / positive regulation of apoptotic signaling pathway / Regulation of PTEN gene transcription / fatty acid metabolic process / placenta development / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / mRNA transcription by RNA polymerase II / PPARA activates gene expression / regulation of circadian rhythm / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / lipid metabolic process / regulation of blood pressure / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / nuclear receptor activity / rhythmic process / glucose homeostasis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / double-stranded DNA binding / DNA-binding transcription factor binding / cellular response to hypoxia / sequence-specific DNA binding / nucleic acid binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / receptor complex / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / negative regulation of gene expression / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II
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 ...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 / 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
S-1,2-PROPANEDIOL / 1-[chloro(dipropyl)-lambda~4~-sulfanyl]propane / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
Authorsle Maire, A. / Bourguet, W.
CitationJournal: To be Published
Title: Crystal structure of PPARgamma ligand binding domain in complex with tripropyltin
Authors: le Maire, A. / Bourguet, W.
History
DepositionNov 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Feb 21, 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

Downloads & links

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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)65,9438
Polymers65,2452
Non-polymers6986
Water4,161231
1
A: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8202
Polymers32,6231
Non-polymers1971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1246
Polymers32,6231
Non-polymers5015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.406, 61.747, 118.659
Angle α, β, γ (deg.)90.00, 102.91, 90.00
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: 32622.746 Da / Num. of mol.: 2 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P37231
#2: Chemical ChemComp-XPT / 1-[chloro(dipropyl)-lambda~4~-sulfanyl]propane


Mass: 196.781 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H21ClS
#3: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.2M tri-sodium citrate, 100mM Hepes, 3.5% 1,2-propanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.35→115.659 Å / Num. all: 26894 / Num. obs: 26894 / % possible obs: 97.2 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 14.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.35-2.482.40.1693.4864035570.16988.9
2.48-2.632.90.1374.11092037800.13799.7
2.63-2.812.90.0985.41035435890.09899.8
2.81-3.032.90.0717.6954232920.07199.8
3.03-3.322.90.0539.8881330600.05399.5
3.32-3.722.90.04113801427970.04199.7
3.72-4.292.80.02919.2692824520.02999.8
4.29-5.252.80.03416.6576920680.03499.6
5.25-7.432.60.03217.2419216270.03299.4
7.43-39.4672.60.02225.217736720.02272.3

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Processing

Software
NameVersionClassificationNB
SCALA3.2.19data scaling
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
MOSFLMdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→33.32 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.35 / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2692 1316 5 %
Rwork0.2008 --
obs0.2042 26301 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.493 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso max: 102.81 Å2 / Biso mean: 41.2753 Å2 / Biso min: 15.47 Å2
Baniso -1Baniso -2Baniso -3
1-6.6926 Å2-0 Å27.3844 Å2
2--10.0061 Å20 Å2
3----16.6987 Å2
Refinement stepCycle: LAST / Resolution: 2.35→33.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4039 0 40 231 4310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084178
X-RAY DIFFRACTIONf_angle_d1.0585640
X-RAY DIFFRACTIONf_chiral_restr0.067656
X-RAY DIFFRACTIONf_plane_restr0.004709
X-RAY DIFFRACTIONf_dihedral_angle_d17.7511556
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.44410.29681270.21182278240579
2.4441-2.55530.29131430.21922731287494
2.5553-2.68990.32781400.21642802294296
2.6899-2.85840.29981390.21082822296198
2.8584-3.07890.32351600.20612870303099
3.0789-3.38850.28671510.20522890304199
3.3885-3.87820.24591380.174329293067100
3.8782-4.88370.20921530.150929313084100
4.8837-33.32340.23111650.19032732289791

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