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- PDB-3ulc: Crystal structure of the pleckstrin homology domain of Saccharomy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ulc | ||||||
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Title | Crystal structure of the pleckstrin homology domain of Saccharomyces cerevisiae Avo1, a TORC2 subunit, in the P3121 crystal form | ||||||
![]() | Target of rapamycin complex 2 subunit AVO1 | ||||||
![]() | MEMBRANE PROTEIN / PH domain / membrane localization | ||||||
Function / homology | ![]() PIP3 activates AKT signaling / CD28 dependent PI3K/Akt signaling / Regulation of TP53 Degradation / TORC2 signaling / establishment or maintenance of actin cytoskeleton polarity / VEGFR2 mediated vascular permeability / TORC2 complex / vacuolar membrane / TOR signaling / phosphatidylinositol-4,5-bisphosphate binding ...PIP3 activates AKT signaling / CD28 dependent PI3K/Akt signaling / Regulation of TP53 Degradation / TORC2 signaling / establishment or maintenance of actin cytoskeleton polarity / VEGFR2 mediated vascular permeability / TORC2 complex / vacuolar membrane / TOR signaling / phosphatidylinositol-4,5-bisphosphate binding / regulation of cell growth / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pan, D. / Matsuura, Y. | ||||||
![]() | ![]() Title: Structures of the pleckstrin homology domain of Saccharomyces cerevisiae Avo1 and its human orthologue Sin1, an essential subunit of TOR complex 2 Authors: Pan, D. / Matsuura, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 33.8 KB | Display | ![]() |
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PDB format | ![]() | 21.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.1 KB | Display | ![]() |
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Full document | ![]() | 425.1 KB | Display | |
Data in XML | ![]() | 5.6 KB | Display | |
Data in CIF | ![]() | 6.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ulbSC ![]() 3voqC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14608.734 Da / Num. of mol.: 1 / Fragment: PH domain, residues 1056-1176 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: S288c / Gene: AVO1 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Tris-HCl, 6% PEG8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2009 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→32.88 Å / Num. all: 4709 / Num. obs: 4563 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.051 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 3.7 / % possible all: 84 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3ULB Resolution: 2.8→28.64 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.838 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15 / SU ML: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.71 Å2 / Biso mean: 57.7293 Å2 / Biso min: 24.63 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→28.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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