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- PDB-4xuh: PPARgamma ligand binding domain in complex with sulindac sulfide -

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Basic information

Entry
Database: PDB / ID: 4xuh
TitlePPARgamma ligand binding domain in complex with sulindac sulfide
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSLATION / Nuclear receptor / PPARgamma / sulindac sulfide / NSAIDs
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 / DNA binding domain binding / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / 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 / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / 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 / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / cell fate commitment / positive regulation of DNA binding / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / regulation of cellular response to insulin stimulus / cell maturation / negative regulation of signaling receptor activity / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / negative regulation of angiogenesis / response to nutrient / negative regulation of miRNA transcription / negative regulation of MAP kinase activity / fatty acid metabolic process / Regulation of PTEN gene transcription / transcription coregulator binding / negative regulation of smooth muscle cell proliferation / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / placenta development / regulation of circadian rhythm / lipid metabolic process / PPARA activates gene expression / regulation of blood pressure / positive regulation of DNA-binding transcription factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / nuclear receptor activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / : / rhythmic process / 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 / intracellular membrane-bounded organelle / innate immune response / 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-SFI / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 Å
AuthorsPuhl, A.C. / Polikaporv, I. / Webb, P.
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 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: 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_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)64,8316
Polymers63,4702
Non-polymers1,3624
Water3,315184
1
A: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4163
Polymers31,7351
Non-polymers6812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4163
Polymers31,7351
Non-polymers6812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.770, 63.630, 119.650
Angle α, β, γ (deg.)90.00, 102.38, 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: 31734.863 Da / Num. of mol.: 2 / Fragment: UNP residues 232-505
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: Chemical
ChemComp-SFI / 2-[(3Z)-6-fluoranyl-2-methyl-3-[(4-methylsulfanylphenyl)methylidene]inden-1-yl]ethanoic acid / sulindac sulfide


Mass: 340.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H17FO2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% (w/v) PEG 6000 and 0.1 M Tris-HCl pH 8.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.19→44.82 Å / Num. obs: 34907 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 38.94 Å2 / Rsym value: 0.066 / Net I/σ(I): 16.1
Reflection shellResolution: 2.19→2.31 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.53 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHASERphasing
PDB_EXTRACT3.15data extraction
SCALAdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SZ1

3sz1


Resolution: 2.22→44.818 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 1695 5.07 %
Rwork0.1865 --
obs0.1888 33459 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→44.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4090 0 96 184 4370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054301
X-RAY DIFFRACTIONf_angle_d0.8725828
X-RAY DIFFRACTIONf_dihedral_angle_d12.5552592
X-RAY DIFFRACTIONf_chiral_restr0.04671
X-RAY DIFFRACTIONf_plane_restr0.004732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.28540.36891460.30632598X-RAY DIFFRACTION99
2.2854-2.35910.30581260.23512667X-RAY DIFFRACTION100
2.3591-2.44340.31131350.22062636X-RAY DIFFRACTION100
2.4434-2.54130.30671440.21862639X-RAY DIFFRACTION100
2.5413-2.65690.28231330.22012655X-RAY DIFFRACTION100
2.6569-2.7970.27271350.21632615X-RAY DIFFRACTION100
2.797-2.97220.26331500.21762604X-RAY DIFFRACTION100
2.9722-3.20160.28131690.2172615X-RAY DIFFRACTION100
3.2016-3.52370.25261370.19232678X-RAY DIFFRACTION100
3.5237-4.03320.18661230.16272664X-RAY DIFFRACTION100
4.0332-5.08030.19041240.14422693X-RAY DIFFRACTION100
5.0803-44.82720.18121730.16912700X-RAY DIFFRACTION100
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)
19.31593.0411-6.42072.5999-0.24339.1097-0.04570.0198-0.3522-0.068-0.0599-0.03470.232-0.39430.06360.26420.0978-0.06580.33770.03460.28620.723-6.365213.9928
28.59462.84721.74864.04940.06426.4486-0.58321.8042-0.0539-0.3810.5080.1923-0.52340.48130.10340.7156-0.0517-0.00210.6908-0.07370.341311.80994.749-3.7481
38.83823.05231.44625.6714.07237.5698-0.29380.16920.6547-1.25480.2696-0.2461-2.52051.2018-0.06511.4065-0.33170.03190.80220.03450.636618.713816.88171.7078
46.45637.5922-6.5228.7843-6.84156.9621-0.34390.59610.1893-0.21910.48040.0427-0.1869-0.1061-0.18770.43210.0364-0.03740.4519-00.282211.66378.813617.8212
52.3091.0317-1.15441.2129-0.5296.6824-0.05240.0139-0.1117-0.03640.0336-0.1804-0.22510.74730.03460.3680.1087-0.0170.42840.00320.346114.76-1.333718.0646
64.03930.4281.52935.09110.06760.49910.2114-0.1947-0.65140.70270.0926-0.16521.95240.1947-0.33420.60670.16550.00770.37140.09490.43655.1412-16.825923.7837
78.23028.61611.15919.49871.73811.05920.1268-0.371-0.36870.1762-0.1562-0.68890.20910.57260.04010.49940.1965-0.03980.65450.03710.433522.8033-3.005121.4491
85.98056.0716-0.37189.42180.55056.90070.3828-0.2669-0.23330.7158-0.2129-0.6335-0.13240.5079-0.12050.55760.0463-0.02870.5607-0.03530.463120.666712.086126.1491
93.79692.97632.46787.4767.23479.03760.1425-0.3141-0.17420.6821-0.2144-0.04511.0551-0.3594-0.03280.44190.00090.00430.28740.0790.386222.3879-36.040434.3951
104.3105-2.7331.8788.09964.16858.0493-0.1297-0.78430.12380.2020.6579-0.51880.10031.4025-0.53750.67230.0271-0.00710.87110.07910.355342.4848-23.900452.0877
112.30760.37820.46381.78741.17824.522-0.0330.14-0.10010.03450.0705-0.0444-0.16810.3702-0.04850.36560.07740.01690.34270.01920.333434.6838-26.274228.866
123.97781.3568-0.42762.56560.52723.60280.0359-0.8460.18720.3071-0.15430.0615-0.37530.30540.08930.64150.0778-0.01050.51520.02630.326933.721-18.061647.8243
132.18810.281-0.26032.13680.09343.03630.03030.07460.1562-0.031-0.10230.2857-0.4219-0.30030.07850.34190.1321-0.010.33340.03070.329222.4143-21.530928.9701
144.6181-6.42692.95968.9845-4.10912.85380.19560.9330.5638-0.0467-0.55140.09820.11550.47010.29140.6567-0.05240.11560.6710.03060.607848.2949-18.404730.1505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 207 through 238 )
2X-RAY DIFFRACTION2chain 'A' and (resid 239 through 251 )
3X-RAY DIFFRACTION3chain 'A' and (resid 252 through 276 )
4X-RAY DIFFRACTION4chain 'A' and (resid 277 through 302 )
5X-RAY DIFFRACTION5chain 'A' and (resid 303 through 402 )
6X-RAY DIFFRACTION6chain 'A' and (resid 403 through 430 )
7X-RAY DIFFRACTION7chain 'A' and (resid 431 through 459 )
8X-RAY DIFFRACTION8chain 'A' and (resid 460 through 477 )
9X-RAY DIFFRACTION9chain 'B' and (resid 207 through 238 )
10X-RAY DIFFRACTION10chain 'B' and (resid 239 through 276 )
11X-RAY DIFFRACTION11chain 'B' and (resid 277 through 333 )
12X-RAY DIFFRACTION12chain 'B' and (resid 334 through 360 )
13X-RAY DIFFRACTION13chain 'B' and (resid 361 through 459 )
14X-RAY DIFFRACTION14chain 'B' and (resid 460 through 477 )

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