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- PDB-2q5s: Crystal Structure of PPARgamma bound to partial agonist nTZDpa -

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Basic information

Entry
Database: PDB / ID: 2q5s
TitleCrystal Structure of PPARgamma bound to partial agonist nTZDpa
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-NZA / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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)63,4474
Polymers62,5912
Non-polymers8572
Water4,756264
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.712, 62.194, 117.956
Angle α, β, γ (deg.)90.000, 101.050, 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-NZA / 5-CHLORO-1-(4-CHLOROBENZYL)-3-(PHENYLTHIO)-1H-INDOLE-2-CARBOXYLIC ACID / NTZDPA


Mass: 428.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H15Cl2NO2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.4M sodium citrate, 0.125M Tris8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Details: mirror
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 39912 / Num. obs: 39912 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 30.79 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Χ2: 0.961 / Net I/σ(I): 33.4
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3805 / Rsym value: 0.344 / Χ2: 0.883 / % possible all: 95.3

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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: 2.05→9.97 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.809 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.194 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1992 5 %RANDOM
Rwork0.197 ---
obs0.199 39571 99.29 %-
all-39571 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.836 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.05→9.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4052 0 56 264 4372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224255
X-RAY DIFFRACTIONr_angle_refined_deg1.3542.0015764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.7015530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61625.027185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43915784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6961518
X-RAY DIFFRACTIONr_chiral_restr0.1470.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023146
X-RAY DIFFRACTIONr_nbd_refined0.2130.22128
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22978
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.296
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4580.212
X-RAY DIFFRACTIONr_mcbond_it0.8571.52691
X-RAY DIFFRACTIONr_mcangle_it1.0224190
X-RAY DIFFRACTIONr_scbond_it1.76731812
X-RAY DIFFRACTIONr_scangle_it2.4154.51563
LS refinement shellResolution: 2.05→2.101 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 109 -
Rwork0.223 2581 -
obs-2690 93.79 %
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)
12.42510.4781-1.82280.2948-0.07522.5224-0.14760.2502-0.2576-0.08160.00950.0681-0.0638-0.22910.13810.0884-0.006-0.02410.0815-0.04160.15080.80947.316413.5069
21.23140.2447-1.04690.129-0.40743.40770.0305-0.04470.01040.01420.0491-0.0256-0.40640.3079-0.07960.1196-0.0814-0.00560.0787-0.04470.108915.379317.341212.7898
31.357-0.0646-0.36210.3165-0.22221.5012-0.075-0.1015-0.3001-0.014-0.0065-0.03820.07950.15040.08150.0713-0.0033-0.00550.0458-0.00480.171710.66942.967821.1796
411.972613.20122.103915.99252.26350.6846-0.03990.0594-0.1486-0.0850.073-0.14390.04090.2139-0.03310.022-0.0369-0.020.07190.01290.149222.93668.072920.8214
514.8534-3.014214.665832.0023-8.610719.8941-1.4253-0.28030.7650.79540.2044-1.2919-2.46860.32691.22090.2415-0.0657-0.06840.1771-0.13860.215220.680822.073426.5366
63.21221.59960.21542.62151.67082.64340.1083-0.3955-0.3150.1923-0.21910.03480.59220.06240.11070.13930.0064-0.00160.05420.03790.078621.7874-21.58435.0866
724.69841.1698-6.51680.0566-0.438515.4861-0.0064-2.4048-2.962-0.911-1.07350.00951.08880.71151.07990.1226-0.22260.12420.39280.03290.257438.3709-8.924453.4984
82.20210.3676-0.30720.57160.39121.14490.1523-0.26130.1958-0.0542-0.05840.07640.01020.1294-0.09380.0849-0.01120.02380.0718-0.03370.087828.4691-9.209332.2328
911.45997.0557-1.52596.4247-1.14710.24870.137-0.18380.28340.3161-0.04190.1282-0.11450.0417-0.0950.0903-0.0118-0.02140.0525-0.02770.145321.7495-1.941430.7313
106.1497-2.6372-2.890629.18640.17391.3992-0.1520.01941.17970.90860.263-0.08130.644-0.3021-0.1110.3208-0.10290.01390.21530.01050.234249.0688-1.47331.887
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA208 - 2405 - 37
2X-RAY DIFFRACTION2AA241 - 35838 - 155
3X-RAY DIFFRACTION3AA359 - 428156 - 225
4X-RAY DIFFRACTION4AA429 - 462226 - 259
5X-RAY DIFFRACTION5AA463 - 477260 - 274
6X-RAY DIFFRACTION6BB207 - 2374 - 34
7X-RAY DIFFRACTION7BB238 - 26635 - 63
8X-RAY DIFFRACTION8BB275 - 42572 - 222
9X-RAY DIFFRACTION9BB426 - 455223 - 252
10X-RAY DIFFRACTION10BB456 - 476253 - 273

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