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

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Basic information

Entry
Database: PDB / ID: 3osi
TitleCrystal structure of PPARgamma ligand binding domain in complex with tetrachloro-bisphenol A (TCBPA)
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / ligand binding protein
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
S-1,2-PROPANEDIOL / 4,4'-propane-2,2-diylbis(2,6-dichlorophenol) / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
Authorsle Maire, A. / Bourguet, W.
CitationJournal: Environ.Health Perspect. / Year: 2011
Title: Peroxisome proliferator-activated receptor Gamma is a target for halogenated analogs of bisphenol A.
Authors: Riu, A. / Grimaldi, M. / le Maire, A. / Bey, G. / Phillips, K. / Boulahtouf, A. / Perdu, E. / Zalko, D. / Bourguet, W. / Balaguer, P.
History
DepositionSep 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 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)65,3614
Polymers64,9192
Non-polymers4422
Water1,63991
1
A: Peroxisome proliferator-activated receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9023
Polymers32,4601
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxisome proliferator-activated receptor gamma


Theoretical massNumber of molelcules
Total (without water)32,4601
Polymers32,4601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.934, 61.742, 118.644
Angle α, β, γ (deg.)90.00, 102.79, 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: 32459.574 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-XDH / 4,4'-propane-2,2-diylbis(2,6-dichlorophenol)


Mass: 366.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12Cl4O2
#3: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#4: 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: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1M tri-sodium citrate, 100 mM Hepes, 3% 1,2-propanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.7→44.67 Å / Num. all: 18247 / Num. obs: 18014 / % possible obs: 98.7 %

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6_289)refinement
REFMACrefinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→44.67 Å / SU ML: 0.38 / σ(F): 0.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 883 5.16 %
Rwork0.1723 --
all0.233 18013 -
obs0.1766 17920 93.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.443 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5555 Å20 Å24.228 Å2
2--9.8852 Å20 Å2
3----12.4407 Å2
Refinement stepCycle: LAST / Resolution: 2.7→44.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3988 0 26 91 4105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084120
X-RAY DIFFRACTIONf_angle_d1.1565564
X-RAY DIFFRACTIONf_dihedral_angle_d19.4661539
X-RAY DIFFRACTIONf_chiral_restr0.069651
X-RAY DIFFRACTIONf_plane_restr0.004704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.86930.33431300.22822490X-RAY DIFFRACTION87
2.8693-3.09070.32321280.22042606X-RAY DIFFRACTION90
3.0907-3.40170.29571560.17812665X-RAY DIFFRACTION94
3.4017-3.89370.2221470.14992791X-RAY DIFFRACTION97
3.8937-4.90460.22461880.1342782X-RAY DIFFRACTION97
4.9046-44.68180.22431340.17062887X-RAY DIFFRACTION97
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)
10.70680.1165-0.11320.17180.29780.6813-0.1822-0.3497-0.6299-0.1176-0.5577-0.22950.1398-0.14150.00520.19660.00560.15120.22320.07130.4111-6.2728-4.486822.7531
22.56281.5689-0.30352.05241.25621.95810.28680.50140.2808-0.04430.34790.0657-0.873-0.53280.56620.23580.20170.06320.06020.16650.15411.387710.073712.9968
35.93262.93480.06532.75230.32060.429-0.67210.6955-0.5874-1.03990.1597-0.42750.03270.1411-0.04830.2560.05090.08350.39340.01050.07868.563113.5612-3.2214
40.293-0.4175-0.66191.20241.55232.47140.5773-0.04630.6644-0.72650.7046-0.6504-0.38610.65420.04890.6603-0.24180.01630.23810.0130.292522.625726.5053-2.8013
51.34580.34070.60090.2593-0.1620.81940.7758-1.20560.7178-0.0286-0.62080.381-0.9158-0.8180.01660.62590.03440.08480.3783-0.12680.438320.43729.59944.9977
60.251-0.28940.32572.2767-0.8290.53460.0332-1.0964-0.08650.21250.98420.8043-0.0967-1.07670.05540.1718-0.1337-0.09160.65560.16250.302418.025523.805614.0747
71.24420.92460.68940.88520.23380.87270.24330.0144-0.104-0.2151-0.2411-0.1709-0.0218-0.1567-0.01860.19490.153-0.01070.1149-0.02050.22574.498815.502422.5458
80.78450.204-0.3090.7961-0.10140.3247-0.19260.1795-0.272-0.06660.1041-0.1602-0.0747-0.0023-0.01620.03690.0652-0.04770.09510.02710.061312.00312.809118.9667
93.0929-0.01960.62120.10020.29210.9783-0.64550.8106-0.7950.3558-0.04290.346-0.12550.4103-0.00430.2142-0.090.08390.406-0.11570.232229.049117.86336.1102
100.79860.9131-0.39640.9923-0.53442.0952-0.24190.4595-0.2790.04820.0188-0.90950.29130.7902-0.169-0.01150.0424-0.01620.32170.05830.273722.66778.854411.529
110.9023-0.11120.0940.6574-0.43680.7524-0.43920.0915-0.27970.04940.1341-0.05460.38150.2146-0.14320.00320.2389-0.04310.14410.11770.17436.42460.440325.7273
120.3435-0.06170.31670.317-0.12160.29070.1359-0.02-0.3790.27290.3294-0.40690.0021-0.17050.00460.26690.1434-0.05080.19280.04590.228913.221-6.233617.2577
130.42270.65940.05681.25890.35180.26140.1635-0.8367-0.19170.6486-0.1922-0.2970.37510.4756-0.00440.13660.0733-0.06240.2842-0.05120.362626.599715.362622.7462
142.71281.3188-1.55971.0817-1.20661.5080.0720.37160.45561.13850.7150.30030.40110.08630.0660.66710.0534-0.06650.1672-0.14780.445424.875529.044821.3595
150.02210.04-0.01440.0777-0.05850.12410.7281-0.5083-0.23521.2838-0.00060.3929-0.15940.8899-0.00180.5736-0.0440.04350.4179-0.10970.281818.945320.075929.2738
161.51911.2288-0.69021.4287-0.9651.61960.143-0.9136-0.36090.65310.170.46710.74030.32940.08090.36520.08540.10260.14630.10370.424913.9934-27.128522.8884
170.1162-0.0712-0.11160.06060.00940.32110.4279-0.0775-0.46060.0487-0.2038-0.29570.47830.38010.00560.24990.0456-0.00790.08380.07370.35525.0856-26.059730.6775
183.4117-0.9781.43441.9923-0.53450.61010.1668-0.7004-0.66650.72010.1970.7122-0.2099-0.40440.0590.40180.12270.03030.1907-0.00040.173226.6367-19.424945.1477
192.0923-1.078-0.85011.67311.11720.9931.0596-0.7642-0.0719-0.7112-0.15180.01360.69240.69780.05960.52160.0083-0.06490.69060.04440.108135.5613-11.352555.3725
200.0976-0.0273-0.02850.00620.0020.1020.1669-0.490.3083-0.06960.1429-0.095-0.6741.3575-0.00440.5135-0.03910.11020.9879-0.00190.370644.0489-8.714955.1066
210.15110.0142-0.07790.2838-0.1870.15260.1049-0.3172-0.4171-1.0039-0.0272-0.03190.2656-0.0107-0.00060.286-0.0189-0.07610.4916-0.02140.264844.8941-4.937242.0692
220.77070.3679-0.28360.42830.20730.4772-0.0495-0.0368-0.64330.21330.20320.04550.30110.34920.00020.20660.09140.01430.1745-0.01380.317834.1514-19.207723.8166
230.750.4332-0.78490.3723-0.08771.7364-0.06160.1371-0.21410.0675-0.2178-0.2175-0.2087-0.1491-0.07860.0810.06880.0140.0405-0.00270.098531.7417-10.864127.4442
242.26290.2862-0.82742.9179-0.45911.4980.7918-0.5063-0.0655-0.3793-0.6090.6344-0.65670.15740.05930.28680.0990.00270.28740.01980.142731.8843-7.66148.3568
250.08760.0234-0.02220.01920.03720.160.4688-0.62071.15180.54960.41440.2045-1.0114-0.0542-0.0090.7196-0.04570.15610.3512-0.04090.21139.53964.609244.0373
260.6450.58710.20961.0040.29220.4835-0.0896-0.01650.4894-0.3435-0.01310.5013-0.3781-0.0916-0.01190.37780.12220.08480.20130.04820.170924.3523-4.37139.7962
271.68510.6969-1.26410.439-1.06292.6078-0.1040.48440.1029-0.25920.00470.054-0.1157-0.3485-0.1390.15360.1256-0.06620.06450.07120.21521.1396-15.146521.7163
280.1419-0.1829-0.00870.22130.00820.0003-0.16330.0182-0.5269-0.04660.0625-0.0867-0.1992-0.1877-0.00020.22520.09330.06410.26310.00850.330410.9101-11.755631.6923
290.4405-0.08370.04590.2144-0.29020.4160.80660.6191.05680.402-0.32670.6288-0.1557-0.0494-0.00020.28090.06510.09570.36490.05290.325630.00820.094829.9329
300.2341-0.6152-0.10351.64570.07460.7410.0711-0.1292-0.2513-1.00020.2547-0.23870.07891.09150.04440.42250.0631-0.06180.24770.0160.21749.5348-2.506531.9353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 205:217)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 218:233)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 234:250)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 251:257)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 258:279)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 280:288)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 289:304)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 305:349)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 350:358)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 359:377)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 378:424)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 425:441)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 442:458)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 459:467)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 468:476)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 208:214)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 215:225)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 226:244)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 245:250)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 251:261)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 275:287)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 288:312)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 313:333)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 334:354)
25X-RAY DIFFRACTION25(CHAIN B AND RESID 355:362)
26X-RAY DIFFRACTION26(CHAIN B AND RESID 363:378)
27X-RAY DIFFRACTION27(CHAIN B AND RESID 379:422)
28X-RAY DIFFRACTION28(CHAIN B AND RESID 423:438)
29X-RAY DIFFRACTION29(CHAIN B AND RESID 439:453)
30X-RAY DIFFRACTION30(CHAIN B AND RESID 454:474)

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