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Open data
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Basic information
Entry | Database: PDB / ID: 2vv1 | ||||||
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Title | hPPARgamma Ligand binding domain in complex with 4-HDHA | ||||||
![]() | (PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA) x 2 | ||||||
![]() | 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 | ![]() 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 | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Itoh, T. / Fairall, L. / Schwabe, J.W.R. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.9 KB | Display | ![]() |
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PDB format | ![]() | 88.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 962 KB | Display | ![]() |
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Full document | ![]() | 971.6 KB | Display | |
Data in XML | ![]() | 22.2 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vsrC ![]() 2vstC ![]() 2vv0C ![]() 2vv2C ![]() 2vv3C ![]() 2vv4C ![]() 2i4pS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31449.520 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 202-475 Source method: isolated from a genetically manipulated source Details: 4-HDHA / Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Protein | Mass: 31465.520 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 202-475 Source method: isolated from a genetically manipulated source Details: 4-HDHA / Source: (gene. exp.) ![]() ![]() ![]() | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | 4-HDHA (4HD): RACEMIC MIX USED IN CRYSTALLIS | Sequence details | RESIDUE NUMBERING CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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 NACITRATE, 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: ![]() ![]() ![]() |
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: 2.2→58.12 Å / Num. obs: 52255 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2I4P Resolution: 2.2→49.27 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1722106.43 / 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: 67.0646 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→49.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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