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- PDB-2q8s: X-ray Crystal structure of the nuclear hormone receptor PPAR-gamm... -

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Basic information

Entry
Database: PDB / ID: 2q8s
TitleX-ray Crystal structure of the nuclear hormone receptor PPAR-gamma in a complex with a PPAR gamma/alpha dual agonist
ComponentsPeroxisome proliferator-activated receptor gamma
Keywordshormone receptor / ligand-bound complex
Function / homology
Function and homology information


prostaglandin receptor 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 / positive regulation of cholesterol transport / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of low-density lipoprotein receptor activity ...prostaglandin receptor 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 / positive regulation of cholesterol transport / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of low-density lipoprotein receptor activity / arachidonate binding / 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 / WW 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 / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / white fat cell differentiation / negative regulation of BMP signaling pathway / cell fate commitment / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / negative regulation of MAPK cascade / BMP signaling pathway / retinoic acid receptor signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cell maturation / epithelial cell differentiation / negative regulation of signaling receptor activity / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / regulation of cellular response to insulin stimulus / negative regulation of angiogenesis / response to nutrient / negative regulation of miRNA transcription / Regulation of PTEN gene transcription / transcription coregulator binding / fatty acid metabolic process / negative regulation of smooth muscle cell proliferation / positive regulation of apoptotic signaling pathway / negative regulation of transforming growth factor beta receptor signaling pathway / peptide binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / regulation of circadian rhythm / placenta development / PPARA activates gene expression / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / positive regulation of miRNA transcription / regulation of blood pressure / cellular response to insulin stimulus / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / 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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / intracellular membrane-bounded organelle / innate immune response / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression
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 / 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-L92 / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsOhren, J.F.
CitationJournal: Bioorg.Med.Chem. / Year: 2008
Title: Effects of modifications of the linker in a series of phenylpropanoic acid derivatives: Synthesis, evaluation as PPARalpha/gamma dual agonists, and X-ray crystallographic studies.
Authors: Casimiro-Garcia, A. / Bigge, C.F. / Davis, J.A. / Padalino, T. / Pulaski, J. / Ohren, J.F. / McConnell, P. / Kane, C.D. / Royer, L.J. / Stevens, K.A. / Auerbach, B.J. / Collard, W.T. / ...Authors: Casimiro-Garcia, A. / Bigge, C.F. / Davis, J.A. / Padalino, T. / Pulaski, J. / Ohren, J.F. / McConnell, P. / Kane, C.D. / Royer, L.J. / Stevens, K.A. / Auerbach, B.J. / Collard, W.T. / McGregor, C. / Fakhoury, S.A. / Schaum, R.P. / Zhou, H.
History
DepositionJun 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)62,4093
Polymers61,9942
Non-polymers4141
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-12.2 kcal/mol
Surface area25030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.455, 62.016, 118.660
Angle α, β, γ (deg.)90.00, 102.54, 90.00
Int Tables number5
Space group name H-MC121
DetailsForms a homdimer in this crystal form that mimics the functional RXR heterodimer.

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Components

#1: Protein Peroxisome proliferator-activated receptor gamma / PPAR-gamma


Mass: 30997.021 Da / Num. of mol.: 2 / Fragment: Ligand binding domain (residue 235-505)
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-L92 / (2S)-3-{4-[3-(5-METHYL-2-PHENYL-1,3-OXAZOL-4-YL)PROPYL]PHENYL}-2-(1H-PYRROL-1-YL)PROPANOIC ACID


Mass: 414.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H26N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Immidizole, 860 mM Sodium Citrate, Glycerol 5 % (v/v) , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→35 Å / Num. all: 29706 / Num. obs: 28675 / % possible obs: 89.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rsym value: 0.056 / Net I/σ(I): 26
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 3509 / Rsym value: 0.375 / % possible all: 52.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2CRK

2crk


Resolution: 2.3→35 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.917 / SU B: 19.306 / SU ML: 0.235 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.352 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28223 1420 5.2 %RANDOM
Rwork0.22239 ---
obs0.2254 26150 92.81 %-
all-29706 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 74.217 Å2
Baniso -1Baniso -2Baniso -3
1--2.53 Å20 Å2-1.76 Å2
2--7.23 Å20 Å2
3----5.47 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4046 0 31 59 4136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224162
X-RAY DIFFRACTIONr_bond_other_d0.0020.023919
X-RAY DIFFRACTIONr_angle_refined_deg1.1431.9985599
X-RAY DIFFRACTIONr_angle_other_deg1.12439164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2035501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.65825.464183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03815809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3451515
X-RAY DIFFRACTIONr_chiral_restr0.060.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024467
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02784
X-RAY DIFFRACTIONr_nbd_refined0.2010.2986
X-RAY DIFFRACTIONr_nbd_other0.160.23841
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22046
X-RAY DIFFRACTIONr_nbtor_other0.0860.22333
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1810.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0390.21
X-RAY DIFFRACTIONr_mcbond_it0.611.53312
X-RAY DIFFRACTIONr_mcbond_other0.0691.51022
X-RAY DIFFRACTIONr_mcangle_it0.6924083
X-RAY DIFFRACTIONr_scbond_it0.88231918
X-RAY DIFFRACTIONr_scangle_it1.3594.51516
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 53 -
Rwork0.312 1315 -
obs--62.87 %
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)
12.19070.193-1.52532.0149-3.69988.1767-0.31960.2062-0.1709-0.16510.28960.106-0.0285-0.71770.03-0.20450.07810.0174-0.19520.01810.00210.47149.72714.042
217.65792.63280.21025.0371-1.36947.09230.18231.33540.97970.40710.31240.4812-0.96080.2298-0.4947-0.1545-0.10870.0872-0.10270.0453-0.254615.15365.677-2.735
335.445213.5162-28.076310.5857-9.6822.43330.38790.96941.70570.11910.37850.4608-0.8896-0.3305-0.7664-0.10550.0031-0.1235-0.070.0135-0.056519.19169.80912.973
42.02721.0072-1.8760.5613-1.08357.6517-0.1532-0.24360.02820.15390.1145-0.0255-0.51350.21820.0387-0.06790.1501-0.0017-0.26310.0125-0.04449.59156.9621.355
56.21366.5032-2.51410.7176-3.60365.5415-0.1968-0.135-0.59370.15380.0478-0.8089-0.17471.28950.149-0.24480.05560.01090.061-0.0371-0.07224.25256.7739.255
61.3769-0.23041.72041.66871.07127.6384-0.2786-0.1853-0.33220.32660.26780.09590.23010.10740.0108-0.11350.21550.0718-0.2010.10110.04786.56145.41126.969
72.99593.8765-0.118211.42971.74661.16360.1335-0.5206-0.26990.4934-0.1252-0.83240.1290.5013-0.0083-0.21550.1617-0.0953-0.0368-0.0265-0.151621.53357.77422.443
82.86320.59032.39253.87132.462711.36620.2189-0.3272-0.60110.4819-0.0457-0.33410.988-0.153-0.1732-0.02680.08460.0679-0.41670.0763-0.052424.04321.61135.023
918.1485-0.41333.145110.75076.144820.32960.6275-0.8213-0.8181.0211-0.3863-0.76290.67321.5127-0.2412-0.33660.1678-0.01340.00450.1225-0.51637.42632.08255.09
106.33488.89428.828144.30334.734835.7062-0.385-0.6836-0.0421-0.08370.91470.1318-0.96642.2093-0.5297-0.1117-0.03540.09780.02420.0216-0.194244.36437.55740.717
111.835-0.3113-0.79780.95171.37317.73280.0319-0.0071-0.09330.14350.0967-0.01520.05310.2933-0.1286-0.07990.13580.0268-0.31960.0107-0.018432.04730.09629.118
1219.75777.67629.73186.24844.28279.1586-0.68820.04671.27940.0390.15920.5317-1.36650.52540.5290.24340.04450.0806-0.29380.0057-0.146930.36242.83443.133
134.25961.669-2.19121.6865-2.24936.17950.08210.3159-0.0605-0.0775-0.08420.219-0.0142-0.26840.0021-0.07330.17560.0155-0.3481-0.03670.032321.43629.27321.598
1419.26252.73172.75592.13410.13651.68890.20380.30881.51960.1521-0.09870.1989-0.28580.2288-0.10510.00520.1110.1058-0.35410.0347-0.163936.37541.95531.035
1524.8459.0852-11.882169.9395-82.377897.0873-0.2759-0.5744-3.2460.7412-0.4555-1.1287-3.6547-1.21170.7314-0.0092-0.052-0.1082-0.22220.07150.156818.17364.01912.906
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA207 - 2381 - 32
2X-RAY DIFFRACTION2AA240 - 26034 - 54
3X-RAY DIFFRACTION3AA276 - 29170 - 85
4X-RAY DIFFRACTION4AA297 - 34591 - 139
5X-RAY DIFFRACTION5AA348 - 378142 - 172
6X-RAY DIFFRACTION6AA381 - 424175 - 218
7X-RAY DIFFRACTION7AA430 - 474224 - 268
8X-RAY DIFFRACTION8BB210 - 2374 - 31
9X-RAY DIFFRACTION9BB240 - 26034 - 54
10X-RAY DIFFRACTION10BB276 - 29170 - 85
11X-RAY DIFFRACTION11BB297 - 34591 - 139
12X-RAY DIFFRACTION12BB348 - 378142 - 172
13X-RAY DIFFRACTION13BB381 - 424175 - 218
14X-RAY DIFFRACTION14BB430 - 474224 - 268
15X-RAY DIFFRACTION15AC10011

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