+Open data
-Basic information
Entry | Database: PDB / ID: 2vv3 | ||||||
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Title | hPPARgamma Ligand binding domain in complex with 4-oxoDHA | ||||||
Components | PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA | ||||||
Keywords | RECEPTOR / NUCLEAR RECEPTOR / TRANSCRIPTION REGULATION / ALTERNATIVE SPLICING / LIGAND BINDING DOMAIN / 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 negative regulation of connective tissue replacement involved in inflammatory response wound healing / prostaglandin receptor activity / 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 / positive regulation of cholesterol transport / negative regulation of cardiac muscle hypertrophy in response to stress / positive regulation of low-density lipoprotein receptor activity ...negative regulation of connective tissue replacement involved in inflammatory response wound healing / prostaglandin receptor activity / 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 / positive regulation of cholesterol transport / negative regulation of cardiac muscle hypertrophy in response to stress / 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 / negative regulation of osteoblast differentiation / positive regulation of fat cell 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 / fatty acid metabolic process / transcription coregulator binding / negative regulation of smooth muscle cell proliferation / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of apoptotic signaling pathway / SUMOylation of intracellular receptors / regulation of circadian rhythm / mRNA transcription by RNA polymerase II / placenta development / lipid metabolic process / PPARA activates gene expression / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / regulation of blood pressure / cellular response to insulin stimulus / positive regulation of miRNA transcription / 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 / intracellular membrane-bounded organelle / innate immune response / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 Ppargamma by Oxidized 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 | 2vv3.cif.gz | 114.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vv3.ent.gz | 88.2 KB | Display | PDB format |
PDBx/mmJSON format | 2vv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vv3_validation.pdf.gz | 660.6 KB | Display | wwPDB validaton report |
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Full document | 2vv3_full_validation.pdf.gz | 673.5 KB | Display | |
Data in XML | 2vv3_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 2vv3_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/2vv3 ftp://data.pdbj.org/pub/pdb/validation_reports/vv/2vv3 | HTTPS FTP |
-Related structure data
Related structure data | 2vsrC 2vstC 2vv0C 2vv1C 2vv2C 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: 4-OXODHA / 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 | ChemComp-4R8 / ( | #3: Water | ChemComp-HOH / | Nonpolymer details | 4-OXODOCOSAH | 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: TRIS 100MM PH 8, 0.7M NA-CITRATE, 1MM TCEP, 0.5MM EDTA, VAPOUR DIFFUSION, DARK, UNDER NITROGEN, 22 DEGREES CELSIUS |
-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: 2.85→58.12 Å / Num. obs: 28148 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 44.2 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.85→3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2I4P Resolution: 2.85→33.61 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1223872.57 / 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: 39.2092 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.85→33.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→3.03 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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