+Open data
-Basic information
Entry | Database: PDB / ID: 7sqa | ||||||
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Title | PPAR gamma LBD bound to SR10221 and SMRT corepressor motif | ||||||
Components |
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Keywords | TRANSCRIPTION / Inverse agonist / Nuclear receptor / Ligand binding domain / corepressor | ||||||
Function / homology | Function and homology information Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor 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 / Notch binding ...Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor 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 / Notch binding / 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 / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of SMAD protein signal transduction / Notch-HLH transcription pathway / 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 / Regulation of MECP2 expression and activity / cellular response to low-density lipoprotein particle stimulus / negative regulation of BMP signaling pathway / white fat cell differentiation / estrous cycle / 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 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / : / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / lactation / transcription repressor complex / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / negative regulation of angiogenesis / cerebellum development / response to nutrient / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / negative regulation of MAP kinase activity / fatty acid metabolic process / Regulation of PTEN gene transcription / transcription coregulator binding / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / 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 / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / regulation of blood pressure / positive regulation of DNA-binding transcription factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / positive regulation of miRNA transcription / histone deacetylase binding / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / HCMV Early Events Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.499 Å | ||||||
Authors | Frkic, R.L. / Pederick, J.L. / Bruning, J.B. | ||||||
Funding support | 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2023 Title: PPAR gamma Corepression Involves Alternate Ligand Conformation and Inflation of H12 Ensembles. Authors: Frkic, R.L. / Pederick, J.L. / Horsfall, A.J. / Jovcevski, B. / Crame, E.E. / Kowalczyk, W. / Pukala, T.L. / Chang, M.R. / Zheng, J. / Blayo, A.L. / Abell, A.D. / Kamenecka, T.M. / Harbort, ...Authors: Frkic, R.L. / Pederick, J.L. / Horsfall, A.J. / Jovcevski, B. / Crame, E.E. / Kowalczyk, W. / Pukala, T.L. / Chang, M.R. / Zheng, J. / Blayo, A.L. / Abell, A.D. / Kamenecka, T.M. / Harbort, J.S. / Harmer, J.R. / Griffin, P.R. / Bruning, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sqa.cif.gz | 240.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sqa.ent.gz | 191.1 KB | Display | PDB format |
PDBx/mmJSON format | 7sqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sqa_validation.pdf.gz | 955.4 KB | Display | wwPDB validaton report |
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Full document | 7sqa_full_validation.pdf.gz | 963.7 KB | Display | |
Data in XML | 7sqa_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 7sqa_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sq/7sqa ftp://data.pdbj.org/pub/pdb/validation_reports/sq/7sqa | HTTPS FTP |
-Related structure data
Related structure data | 7sqbC 6pdzS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33300.520 Da / Num. of mol.: 2 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: Protein/peptide | Mass: 2599.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y618 #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.84 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 28% PEG 8,000, 0.1M Ammonium sulphate, 0.1M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95373 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 23, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.499→43.87 Å / Num. obs: 22167 / % possible obs: 98.2 % / Redundancy: 3.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.092 / Rrim(I) all: 0.169 / Net I/σ(I): 4.5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6pdz Resolution: 2.499→41.884 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 211.84 Å2 / Biso mean: 64.7404 Å2 / Biso min: 15.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.499→41.884 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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