+Open data
-Basic information
Entry | Database: PDB / ID: 2vv2 | ||||||
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Title | hPPARgamma Ligand binding domain in complex with 5-HEPA | ||||||
Components | PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA | ||||||
Keywords | RECEPTOR / TRANSCRIPTION REGULATION / ALTERNATIVE SPLICING / LIGAND BINDING DOMAIN / NUCLEAR RECEPTOR / DIABETES MELLITUS / ZINC-FINGER / DNA-BINDING / POLYMORPHISM / TRANSCRIPTION / ZINC / OBESITY / NUCLEUS / ACTIVATOR / OXIDISED FATTY ACID / TRANSCRIPTION FACTOR / METAL-BINDING / PHOSPHOPROTEIN / DISEASE MUTATION | ||||||
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 / positive regulation of vascular associated smooth muscle cell apoptotic process / macrophage derived foam cell differentiation / DNA binding 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 / negative regulation of blood vessel endothelial cell migration / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / positive regulation of cholesterol efflux / cellular response to low-density lipoprotein particle stimulus / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / long-chain fatty acid transport / retinoic acid receptor signaling pathway / positive regulation of DNA binding / cell fate commitment / BMP signaling pathway / nuclear retinoid X receptor binding / negative regulation of signaling receptor activity / regulation of cellular response to insulin stimulus / cell maturation / positive regulation of adipose tissue development / epithelial cell differentiation / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / negative regulation of angiogenesis / response to nutrient / negative regulation of MAP kinase activity / fatty acid metabolic process / negative regulation of miRNA transcription / placenta development / Regulation of PTEN gene transcription / negative regulation of smooth muscle cell proliferation / transcription coregulator binding / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / lipid metabolic process / regulation of circadian rhythm / PPARA activates gene expression / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of blood pressure / Transcriptional regulation of white adipocyte differentiation / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / activation of cysteine-type endopeptidase activity involved in apoptotic process / rhythmic process / nuclear receptor activity / : / positive regulation of DNA-binding transcription factor activity / 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 / cell differentiation / nucleic acid binding / 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 / innate immune response / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Itoh, T. / Fairall, L. / Schwabe, J.W.R. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: Structural Basis for the Activation of Pparg by Oxidised Fatty Acids Authors: Itoh, T. / Fairall, L. / Amin, K. / Inaba, Y. / Szanto, A. / Balint, B.L. / Nagy, L. / Yamamoto, K. / Schwabe, J.W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vv2.cif.gz | 117 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vv2.ent.gz | 91.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/2vv2 ftp://data.pdbj.org/pub/pdb/validation_reports/vv/2vv2 | HTTPS FTP |
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-Related structure data
Related structure data | 2vsrC 2vstC 2vv0C 2vv1C 2vv3C 2vv4C 2i4pS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31449.520 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 202-475 Source method: isolated from a genetically manipulated source Details: 5-HEPA / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET30A MODIFIED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: P37231 #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | 5-HYDROXYEIC | Sequence details | RESIDUE NUMBERING CORRESPOND | |
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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: 2.8 Å3/Da / Density % sol: 55.5 % / Description: NONE |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 8 Details: PH 8, TRIS 100MM, 0.7M NA CITRATE, 1MM TCEP, 0.5MM EDTA, VAPOUR DIFFUSION, DARK, UNDER NITROGEN, 22 DEGREES CELCIUS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 16, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→58.32 Å / Num. obs: 32564 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2I4P Resolution: 2.75→36.15 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1295444.51 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.8453 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→36.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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