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- PDB-6c5t: PPARg LBD bound to SR11023 -

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Basic information

Entry
Database: PDB / ID: 6c5t
TitlePPARg LBD bound to SR11023
ComponentsPeroxisome proliferator-activated receptor gamma
KeywordsTRANSCRIPTION / peroxisome proliferator activated receptor gamma / PPARG / nuclear receptor / inverse agonist
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 / DNA binding domain binding / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / 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 macrophage derived foam cell differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / cell fate commitment / positive regulation of DNA binding / BMP signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / regulation of cellular response to insulin stimulus / cell maturation / negative regulation of signaling receptor activity / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / negative regulation of angiogenesis / response to nutrient / negative regulation of miRNA transcription / negative regulation of MAP kinase activity / fatty acid metabolic process / Regulation of PTEN gene transcription / transcription coregulator binding / negative regulation of smooth muscle cell proliferation / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / placenta development / regulation of circadian rhythm / lipid metabolic process / PPARA activates gene expression / regulation of blood pressure / positive regulation of DNA-binding transcription factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / nuclear receptor activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / : / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / intracellular membrane-bounded organelle / innate immune response / 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
Chem-EKP / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsBruning, J.B. / Frkic, R.L. / Griffin, P.R.
CitationJournal: iScience / Year: 2018
Title: PPAR gamma in Complex with an Antagonist and Inverse Agonist: a Tumble and Trap Mechanism of the Activation Helix.
Authors: Frkic, R.L. / Marshall, A.C. / Blayo, A.L. / Pukala, T.L. / Kamenecka, T.M. / Griffin, P.R. / Bruning, J.B.
History
DepositionJan 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0732
Polymers31,5651
Non-polymers5091
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.640, 63.640, 365.350
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-622-

HOH

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Components

#1: Protein Peroxisome proliferator-activated receptor gamma / PPAR-gamma / Nuclear receptor subfamily 1 group C member 3


Mass: 31564.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37231
#2: Chemical ChemComp-EKP / 2-{4-[(5-{[(1R)-1-(3-cyclopropylphenyl)ethyl]carbamoyl}-2,3-dimethyl-1H-indol-1-yl)methyl]phenyl}-2-methylpropanoic acid


Mass: 508.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H36N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.4 Å3/Da / Density % sol: 63.81 % / Description: irregular
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 3350 + 0.2M ammonium citrate 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 18, 2015
RadiationMonochromator: Double Si with sagittaly bent second crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.75→19.71 Å / Num. obs: 12318 / % possible obs: 99.1 % / Redundancy: 8.1 % / Biso Wilson estimate: 70.78 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.241 / Rpim(I) all: 0.08 / Rrim(I) all: 0.256 / Net I/σ(I): 6.5 / Num. measured all: 100208 / Scaling rejects: 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.75-2.928.62.58619320.1360.8312.73899.7
8.25-19.717.70.0385340.9990.0140.0492.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.3.11data scaling
PHASERphasing
PHENIX1.11_2567refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R06

4r06


Resolution: 2.75→19.71 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.13
RfactorNum. reflection% reflection
Rfree0.2861 604 4.98 %
Rwork0.2541 --
obs0.2558 12139 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 237.58 Å2 / Biso mean: 97.3188 Å2 / Biso min: 40.14 Å2
Refinement stepCycle: final / Resolution: 2.75→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2036 0 38 73 2147
Biso mean--90.96 78.83 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012116
X-RAY DIFFRACTIONf_angle_d0.4572875
X-RAY DIFFRACTIONf_chiral_restr0.036337
X-RAY DIFFRACTIONf_plane_restr0.002366
X-RAY DIFFRACTIONf_dihedral_angle_d8.5811262
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7501-3.0260.4161330.40092749288297
3.026-3.46180.34281570.33752810296799
3.4618-4.35380.32141470.25392884303199
4.3538-19.71010.23131670.20353092325998
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)
15.12332.0509-2.91133.2984-1.56972.00360.13680.6879-0.5408-0.37710.2175-0.1159-0.3161-0.1769-0.39770.71560.0682-0.02650.7219-0.09750.553240.5856-22.19155.9397
28.86951.75552.66038.9356-0.73387.32780.1959-1.97630.32392.62790.1036-0.25481.6828-0.6623-0.55171.2508-0.2404-0.13640.731-0.06070.76615.3452-35.644420.0423
32.00224.7691-4.53153.8054-1.77262.24230.1287-1.1747-0.3107-0.1322-0.5409-0.01520.24190.2414-0.13520.981-0.0947-0.13160.505-0.28770.611325.5775-20.024521.4089
43.74183.6830.81174.69061.54822.99730.8278-0.24640.41820.2221-0.41470.0906-0.4096-0.87030.08580.75420.05450.0030.6083-0.19430.428222.8414-18.614412.2862
54.20822.6846-0.57117.781.21284.84990.33590.2750.7512-0.0981-0.04450.1203-0.9194-0.2081-0.41440.71110.2295-0.01110.5722-0.04170.380931.8014-10.67384.2593
69.0327-4.21354.19773.0934-4.66278.42770.00060.511.26261.465-0.4661-0.5211-0.4289-0.36810.84271.2752-0.4567-0.11731.2785-0.19950.886420.2833-18.966532.4504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 202 through 237 )A202 - 237
2X-RAY DIFFRACTION2chain 'A' and (resid 238 through 275 )A238 - 275
3X-RAY DIFFRACTION3chain 'A' and (resid 276 through 302 )A276 - 302
4X-RAY DIFFRACTION4chain 'A' and (resid 303 through 377 )A303 - 377
5X-RAY DIFFRACTION5chain 'A' and (resid 378 through 456 )A378 - 456
6X-RAY DIFFRACTION6chain 'A' and (resid 457 through 477 )A457 - 477

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