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- PDB-4xum: PPARgamma ligand binding domain in complex with indomethacin -

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Basic information

Entry
Database: PDB / ID: 4xum
TitlePPARgamma ligand binding domain in complex with indomethacin
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSLATION / PPARgamma / Nuclear receptor / transcription factor / NSAIDs / indomethacin
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 / negative regulation of macrophage derived foam cell differentiation / cellular response to low-density lipoprotein particle stimulus / 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 / nucleic acid binding / cell differentiation / 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
INDOMETHACIN / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsPuhl, A.C. / Webb, P. / Polikarpov, I.
CitationJournal: Nucl Recept Signal / Year: 2015
Title: Mechanisms of peroxisome proliferator activated receptor gamma regulation by non-steroidal anti-inflammatory drugs.
Authors: Puhl, A.C. / Milton, F.A. / Cvoro, A. / Sieglaff, D.H. / Campos, J.C. / Bernardes, A. / Filgueira, C.S. / Lindemann, J.L. / Deng, T. / Neves, F.A. / Polikarpov, I. / Webb, P.
History
DepositionJan 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: 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_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)64,5435
Polymers63,4702
Non-polymers1,0733
Water1,18966
1
A: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4503
Polymers31,7351
Non-polymers7162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0932
Polymers31,7351
Non-polymers3581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.040, 62.140, 118.540
Angle α, β, γ (deg.)90.000, 102.130, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 207 - 477 / Label seq-ID: 8 - 278

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

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


Mass: 31734.863 Da / Num. of mol.: 2
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: Chemical ChemComp-IMN / INDOMETHACIN / Indometacin


Mass: 357.788 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H16ClNO4 / Comment: medication, antiinflammatory*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.95 M sodium citrate and 0.1 M HEPES pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.4→115.893 Å / Num. all: 26080 / Num. obs: 26080 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 51.11 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.079 / Rsym value: 0.069 / Net I/av σ(I): 6.683 / Net I/σ(I): 12.1 / Num. measured all: 116570
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.4-2.534.40.5021.51684837990.2730.5022.8100
2.53-2.684.40.3312.31598935970.1790.3314100
2.68-2.874.50.2113.51486333300.1150.2116100
2.87-3.14.50.1435.11421231700.0770.1438.4100
3.1-3.394.50.08281295728790.0450.08213.3100
3.39-3.794.50.0639.11184126180.0340.06318.2100
3.79-4.384.50.06191057223380.0330.06122.4100
4.38-5.374.50.05810.1892919790.0310.05823.8100
5.37-7.594.50.04711.9689615350.0250.04724.1100
7.59-36.3374.10.03915.434638350.0220.03926.594.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→36.337 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 1322 5.08 %random
Rwork0.1878 24714 --
obs0.1905 26036 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 209.14 Å2 / Biso mean: 74.8187 Å2 / Biso min: 35.34 Å2
Refinement stepCycle: final / Resolution: 2.4→36.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3983 0 75 66 4124
Biso mean--102.51 57.9 -
Num. residues----520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074163
X-RAY DIFFRACTIONf_angle_d1.0765660
X-RAY DIFFRACTIONf_chiral_restr0.043664
X-RAY DIFFRACTIONf_plane_restr0.005719
X-RAY DIFFRACTIONf_dihedral_angle_d13.2151494
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2154X-RAY DIFFRACTION9.925TORSIONAL
12B2154X-RAY DIFFRACTION9.925TORSIONAL
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 (%)
2.4-2.49610.31021510.256427182869100
2.4961-2.60970.3461500.241227132863100
2.6097-2.74720.25641510.225527292880100
2.7472-2.91930.3151370.217627382875100
2.9193-3.14450.31891270.240827462873100
3.1445-3.46080.30251430.215827722915100
3.4608-3.9610.24621440.172227552899100
3.961-4.98840.19371630.150827472910100
4.9884-36.34080.19871560.17282796295299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1872-0.2168-1.34532.196-1.2097.0739-0.1888-0.3609-0.11520.21710.4480.4378-0.1482-0.6312-0.23970.39810.1084-0.00260.60560.08710.46390.6967-6.002213.7797
24.8854.00056.87976.40515.69869.74070.05682.13730.49430.2480.1560.4193-0.5918-0.0002-0.06890.59-0.05320.02510.78140.01220.442311.32775.2232-3.8404
38.07462.32414.99976.43691.23917.1686-0.51130.71910.7502-0.29810.16130.0046-1.87350.85880.24221.5667-0.45220.13440.86250.03540.774719.47116.8230.5109
44.19933.958-5.57435.7626-4.16058.3553-0.22340.06030.8841-0.0620.42840.3935-0.96530.1651-0.23050.74510.0897-0.12130.71330.01590.499312.29819.274317.4346
52.51961.0898-1.7342.3576-0.79516.7045-0.2656-0.3663-0.22350.02740.1067-0.3082-0.23280.87620.1670.44270.0984-0.0130.58350.04110.407216.57060.904915.539
62.18871.3569-0.05051.6544-0.64146.8008-0.2033-0.6721-0.25470.350.2227-0.29890.34990.73050.11790.46640.240.02830.63330.14840.49838.7432-7.35425.0928
73.02650.74441.54735.01721.39962.3847-0.1469-0.5361-0.69830.63790.5581-0.09931.2633-0.0974-0.45730.63270.20570.0430.63950.22430.70074.828-16.547323.8766
85.85394.83010.0484.1720.43362.1312-0.0195-0.589-0.87960.3228-0.014-1.38280.31380.82290.16040.52490.1976-0.02890.81060.13830.650522.738-3.247121.5802
97.79414.5899-1.36487.61521.60441.3970.5498-1.3890.40711.2708-0.34140.0441-0.130.7436-0.01640.74430.0447-0.0670.984-0.09530.538521.010112.02525.7967
106.23971.61343.67871.83040.67539.47280.107-0.6295-0.62660.3183-0.001-0.12880.5663-0.5707-0.14540.77210.14470.04360.45180.11860.534322.7705-34.910633.4443
114.36171.05651.68852.220.2043.58860.0372-1.007-0.00630.7696-0.1138-0.1334-0.10191.00870.02340.88510.11220.02731.14110.04460.584841.1082-23.719343.1892
125.22281.132-0.93481.0113-2.01186.73-0.0626-0.1243-0.29160.16860.0389-0.0201-0.35340.1689-0.02870.56130.2060.00940.41780.04010.480131.8793-25.284923.5238
137.9174.825-2.57994.8413-3.692.22970.3-1.0170.52150.5405-0.21220.0779-1.03691.1746-0.11431.281-0.0260.08370.9841-0.06040.512634.9524-16.053646.5613
142.80370.1106-0.22632.2618-1.2645.7573-0.0334-0.2216-0.17710.1143-0.00280.4728-0.1828-0.40150.03990.55560.21330.04550.48720.05550.569420.1105-24.538227.0862
152.77463.3934-1.34974.599-1.61988.38450.5075-0.07130.81790.6327-0.2638-0.153-2.01040.447-0.18860.81750.0447-00.53570.00730.794527.9759-13.34229.8209
165.8934-4.8655-5.42584.51284.65885.1094-0.0883-0.72880.9963-0.31060.67140.7482-2.10661.3551-0.61731.2284-0.04710.06560.95640.02980.718850.8396-17.447231.7603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 207 through 238 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 239 through 251 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 252 through 276 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 277 through 302 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 303 through 377 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 378 through 402 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 403 through 430 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 431 through 459 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 460 through 477 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 207 through 237 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 238 through 302 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 303 through 333 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 334 through 364 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 365 through 430 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 431 through 459 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 460 through 477 )B0

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