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- PDB-2q6r: Crystal structure of PPAR gamma complexed with partial agonist SF147 -

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Basic information

Entry
Database: PDB / ID: 2q6r
TitleCrystal structure of PPAR gamma complexed with partial agonist SF147
ComponentsPeroxisome Proliferator-Activated Receptor gamma
KeywordsLigand binding protein / Protein-ligand 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-SF2 / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.407 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: 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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)63,4384
Polymers62,5912
Non-polymers8482
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.800, 62.255, 118.071
Angle α, β, γ (deg.)90.000, 101.120, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUASPASP3AA207 - 2604 - 57
21GLUGLUASPASP3BB207 - 2604 - 57
32LYSLYSLEULEU4AA275 - 47672 - 273
42LYSLYSLEULEU4BB275 - 47672 - 273

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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-SF2 / 5-CHLORO-1-(3-METHOXYBENZYL)-3-(PHENYLTHIO)-1H-INDOLE-2-CARBOXYLIC ACID / SF147


Mass: 423.912 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H18ClNO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.4M sodium citrate, 0.125M 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: 22911 / Num. obs: 22911 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 57.39 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Χ2: 1.111 / Net I/σ(I): 24.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 4.8 / Num. unique all: 1413 / Rsym value: 0.196 / Χ2: 1.194 / % possible all: 56.8

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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: 2.407→10 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.898 / SU B: 22.435 / SU ML: 0.288 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1146 5.1 %RANDOM
Rwork0.269 ---
obs0.27 22642 90.91 %-
all-22642 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20.07 Å2
2--6.03 Å20 Å2
3----6.69 Å2
Refinement stepCycle: LAST / Resolution: 2.407→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3887 0 58 124 4069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224010
X-RAY DIFFRACTIONr_angle_refined_deg1.6162.0045408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.5925486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.92925.46174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.7315742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9541515
X-RAY DIFFRACTIONr_chiral_restr0.2280.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022935
X-RAY DIFFRACTIONr_nbd_refined0.2340.22011
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22785
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3220.2148
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.26
X-RAY DIFFRACTIONr_mcbond_it5.59342453
X-RAY DIFFRACTIONr_mcangle_it9.54843945
X-RAY DIFFRACTIONr_scbond_it6.91561557
X-RAY DIFFRACTIONr_scangle_it10.9737.51463
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
212TIGHT POSITIONAL0.230.05
1382MEDIUM POSITIONAL1.320.5
202LOOSE POSITIONAL0.995
212TIGHT THERMAL15.480.5
1382MEDIUM THERMAL28.662
202LOOSE THERMAL17.8510
LS refinement shellResolution: 2.407→2.466 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 39 -
Rwork0.343 885 -
obs-924 53.1 %
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)
10.17220.4159-0.28291.0811-0.36271.79940.03030.11760.06840.06530.00190.17890.043-0.545-0.03220.17930.0009-0.01260.1452-0.01870.2522-12.027110.301-16.7198
20.95280.1366-0.1980.45920.0280.63740.08780.06430.0756-0.0428-0.04260.051-0.0839-0.0535-0.04510.17010.0069-0.0329-0.00510.00660.2265-29.9718-10.0168-34.6744
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA207 - 4764 - 273
2X-RAY DIFFRACTION2BB207 - 4774 - 274

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