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- PDB-2q6s: 2.4 angstrom crystal structure of PPAR gamma complexed to BVT.13 ... -

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Basic information

Entry
Database: PDB / ID: 2q6s
Title2.4 angstrom crystal structure of PPAR gamma complexed to BVT.13 without co-activator peptides
ComponentsPeroxisome Proliferator-Activated Receptor gamma
KeywordsLigand binding protein / Protein-ligand complex
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 / positive regulation of fatty acid metabolic process / STAT family protein binding / response to lipid / negative regulation of type II interferon-mediated signaling pathway / LBD domain binding / negative regulation of cholesterol storage / negative regulation of SMAD protein signal transduction / E-box binding / lipid homeostasis / alpha-actinin binding / R-SMAD binding / negative regulation of vascular associated smooth muscle cell proliferation / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / white fat cell differentiation / 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 / positive regulation of cholesterol efflux / cell fate commitment / negative regulation of osteoblast differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / 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 / negative regulation of MAPK cascade / intracellular receptor signaling pathway / hormone-mediated signaling pathway / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / response to nutrient / epithelial cell differentiation / regulation of cellular response to insulin stimulus / peptide binding / negative regulation of miRNA transcription / negative regulation of angiogenesis / placenta development / positive regulation of apoptotic signaling pathway / Regulation of PTEN gene transcription / transcription coregulator binding / SUMOylation of intracellular receptors / negative regulation of smooth muscle cell proliferation / mRNA transcription by RNA polymerase II / fatty acid metabolic process / negative regulation of transforming growth factor beta receptor signaling pathway / PPARA activates gene expression / regulation of circadian rhythm / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / lipid metabolic process / positive regulation of miRNA transcription / regulation of blood pressure / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / nuclear receptor activity / cellular response to insulin stimulus / rhythmic process / glucose homeostasis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to hypoxia / DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / receptor complex / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / innate immune response / 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
Chem-PLB / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBruning, J.B. / Nettles, K.W.
CitationJournal: Structure / Year: 2007
Title: Partial Agonists Activate PPARgamma Using a Helix 12 Independent Mechanism
Authors: Bruning, J.B. / Chalmers, M.J. / Prasad, S. / Busby, S.A. / Kamenecka, T.M. / He, Y. / Nettles, K.W. / Griffin, P.R.
History
DepositionJun 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 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_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

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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)62,9953
Polymers62,5912
Non-polymers4041
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.348, 62.033, 118.132
Angle α, β, γ (deg.)90.000, 102.290, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peroxisome Proliferator-Activated Receptor gamma / PPAR-gamma


Mass: 31295.314 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: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: P37231
#2: Chemical ChemComp-PLB / 2-[(2,4-DICHLOROBENZOYL)AMINO]-5-(PYRIMIDIN-2-YLOXY)BENZOIC ACID / 5-(2-PYRIMIDINYLOXY)-2-BENZOYLAMINOBENZOIC ACID


Mass: 404.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H11Cl2N3O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 53.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.4M sodium citrate, 0.125 M Tris 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9764 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Details: mirrors
RadiationMonochromator: Si 220 Rosenbaum-Rock double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. all: 23288 / Num. obs: 23288 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 59.22 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Χ2: 1.116 / Net I/σ(I): 26.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 0.076 / Num. unique all: 1486 / Rsym value: 0.173 / Χ2: 1.128 / % possible all: 59.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KNU

1knu


Resolution: 2.4→10 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 17.359 / SU ML: 0.219 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.579 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2273 9.9 %RANDOM
Rwork0.206 ---
obs0.212 22984 90.58 %-
all-22984 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.708 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å2-0.13 Å2
2--4.37 Å20 Å2
3----5.07 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4061 0 27 151 4239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224204
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.9975663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1055509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9125.326184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81215815
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4381516
X-RAY DIFFRACTIONr_chiral_restr0.0780.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023067
X-RAY DIFFRACTIONr_nbd_refined0.2170.22086
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22972
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2182
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.29
X-RAY DIFFRACTIONr_mcbond_it2.08742632
X-RAY DIFFRACTIONr_mcangle_it2.62644141
X-RAY DIFFRACTIONr_scbond_it3.57661746
X-RAY DIFFRACTIONr_scangle_it4.9997.51522
LS refinement shellResolution: 2.4→2.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 97 -
Rwork0.252 815 -
obs-912 51.12 %
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)
15.25555.7443-2.48876.3417-3.18644.6266-0.5242-0.2282-0.36970.04190.2368-0.02210.3662-0.51380.28740.24020.1560.20850.20020.10390.2511-4.343441.431521.2474
21.11910.17831.26990.6144-0.14381.6455-0.29760.42940.0088-0.24660.43680.1321-0.23310.2129-0.13920.2616-0.00170.05460.26230.04680.18547.70554.85192.9988
39.9671.45126.53343.23134.018621.5538-0.69950.31060.374-0.74920.1546-0.3405-3.00922.10930.54490.6247-0.3391-0.00850.16220.05510.253722.157969.64124.8925
43.57191.1448-3.02841.1029-0.18914.23860.0529-0.49890.20670.19190.04970.2754-0.32980.4665-0.10250.22230.19030.0430.20690.02460.13077.179757.033326.7446
52.39431.3899-4.43372.27490.984216.8325-0.3617-0.2106-0.0963-0.15620.2425-0.11610.08611.26030.11920.10790.1450.05790.28880.05130.133115.742752.134112.955
61.80511.1871-1.50512.97740.6333.8715-0.29890.1018-0.0848-0.11560.2702-0.2777-0.32611.15750.02860.191-0.02030.03610.48440.02610.13923.332957.93757.6969
72.1151.2736-0.71674.193-0.92740.3146-0.4788-0.084-0.5663-0.34030.2966-0.06150.45790.30010.18220.26740.20360.16970.1790.05640.232811.130942.777111.6372
82.95750.5261-0.72562.81472.52135.3414-0.3069-0.4303-0.46110.36580.17660.03140.67070.4270.13030.31070.31250.10650.18390.15540.19576.864541.246426.6509
95.13215.6881-0.032511.04070.9241.44820.0157-0.4762-0.30680.23330.0328-0.67140.16450.7271-0.04860.14650.2360.01120.44660.03270.170822.965752.594220.9671
1020.2722-3.77812.42533.7987-2.092618.17460.8095-2.19661.2970.998-0.9476-0.8583-1.86412.47930.13810.2119-0.25340.10890.5706-0.07550.074517.067764.694126.9905
1145.0062-5.80339.365213.08940.6242.22060.50550.0649-1.6016-1.03440.12630.85950.2532-0.3569-0.63170.3310.0295-0.1137-0.00640.00220.551514.214115.136623.8084
125.46851.28453.00131.5862.28826.98440.2025-1.0612-0.70310.1898-0.07130.02310.4090.2018-0.13110.23450.13930.10070.25740.21130.138631.81324.268546.5263
134.187-4.66211.99168.73534.20712.593-0.6897-0.25840.11340.43751.167-0.2970.05381.8316-0.47730.15890.10980.07570.5348-0.04390.010546.75132.879745.7076
144.05616.27780.049115.19689.591316.5211-0.3561-0.0364-0.04430.00960.61440.3750.1311.7705-0.25830.16560.09120.08590.37420.00160.015442.763431.165937.9918
153.3289-0.3456-0.01910.2571-0.07243.12490.04660.2393-0.3329-0.09640.07290.11450.11930.4457-0.11950.17540.16660.04920.0894-0.0320.177333.606525.798623.3757
164.74320.07740.33451.82981.65174.8969-0.0965-0.66170.2123-0.00060.03150.1152-0.50890.40110.0650.28390.09830.09480.24130.02590.052333.861635.891845.9509
172.7861-0.52440.83640.7064-0.27972.80070.05180.1306-0.10460.02740.07480.2417-0.4471-0.2408-0.12660.20270.15610.10010.02730.03570.156724.786131.600328.3417
183.83890.53040.39281.9526-2.17995.21340.22720.0049-0.40580.06630.16560.6859-0.0633-0.5701-0.39280.11960.13260.0650.10320.07690.353412.559627.353428.3332
1928.20268.75757.42585.1869-0.76387.18630.4646-0.10521.31370.2209-0.45060.4488-0.72410.3417-0.01390.18680.0430.1252-0.030.0070.264832.328342.439630.15
2027.30960.8684-1.43490.9979-3.618613.2327-0.0849-1.16790.2795-0.3329-0.27960.43-1.05261.48670.36460.3936-0.04360.17060.2174-0.04960.104350.633734.02530.1172
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA207 - 2214 - 18
2X-RAY DIFFRACTION2AA222 - 25119 - 48
3X-RAY DIFFRACTION3AA252 - 28449 - 81
4X-RAY DIFFRACTION4AA285 - 32082 - 117
5X-RAY DIFFRACTION5AA321 - 339118 - 136
6X-RAY DIFFRACTION6AA340 - 370137 - 167
7X-RAY DIFFRACTION7AA371 - 385168 - 182
8X-RAY DIFFRACTION8AA386 - 428183 - 225
9X-RAY DIFFRACTION9AA429 - 465226 - 262
10X-RAY DIFFRACTION10AA466 - 474263 - 271
11X-RAY DIFFRACTION11BB207 - 2164 - 13
12X-RAY DIFFRACTION12BB217 - 26014 - 57
13X-RAY DIFFRACTION13BB261 - 28258 - 79
14X-RAY DIFFRACTION14BB283 - 28880 - 85
15X-RAY DIFFRACTION15BB289 - 32786 - 124
16X-RAY DIFFRACTION16BB328 - 361125 - 158
17X-RAY DIFFRACTION17BB362 - 409159 - 206
18X-RAY DIFFRACTION18BB410 - 438207 - 235
19X-RAY DIFFRACTION19BB439 - 456236 - 253
20X-RAY DIFFRACTION20BB466 - 475263 - 272

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