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- PDB-6y3r: 14-3-3 Sigma in complex with phosphorylated (Thr391) Gab2 peptide -
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Open data
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Basic information
Entry | Database: PDB / ID: 6y3r | ||||||
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Title | 14-3-3 Sigma in complex with phosphorylated (Thr391) Gab2 peptide | ||||||
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![]() | PROTEIN BINDING / 14-3-3 / Gab2 / complex / protein / protein-protein interactions | ||||||
Function / homology | ![]() STAT5 Activation / positive regulation of mast cell degranulation / phosphatidylinositol-3,4-bisphosphate binding / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / regulation of epidermal cell division / protein kinase C inhibitor activity / STAT5 activation downstream of FLT3 ITD mutants / positive regulation of epidermal cell differentiation ...STAT5 Activation / positive regulation of mast cell degranulation / phosphatidylinositol-3,4-bisphosphate binding / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / regulation of epidermal cell division / protein kinase C inhibitor activity / STAT5 activation downstream of FLT3 ITD mutants / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / phosphatidylinositol-3,4,5-trisphosphate binding / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / RET signaling / PI3K Cascade / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / RHO GTPases activate PKNs / protein kinase A signaling / protein sequestering activity / Signaling by FLT3 fusion proteins / FLT3 Signaling / negative regulation of innate immune response / protein export from nucleus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / osteoclast differentiation / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Signaling by SCF-KIT / Constitutive Signaling by Aberrant PI3K in Cancer / Signaling by CSF1 (M-CSF) in myeloid cells / intrinsic apoptotic signaling pathway in response to DNA damage / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / regulation of cell cycle / cadherin binding / membrane raft / positive regulation of cell population proliferation / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ballone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A new soaking procedure for X-ray crystallographic structural determination of protein-peptide complexes. Authors: Ballone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90 KB | Display | ![]() |
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PDB format | ![]() | 53.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.8 KB | Display | ![]() |
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Full document | ![]() | 437.4 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 25.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6y3mC ![]() 6y3oC ![]() 6y3sC ![]() 6y3vC ![]() 6y40C ![]() 6y44C ![]() 6y8aC ![]() 6y8bC ![]() 6y8dC ![]() 6y8eC ![]() 3lw1S 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 on special symmetry positions |
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Components
#1: Protein | Mass: 28226.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein/peptide | Mass: 1453.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 28% (v/v) PEG400, 1.25% glycerol, 0.2M CaCl, 0.1M HEPES pH 7.5, 2mM BME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→66.37 Å / Num. obs: 33470 / % possible obs: 72.1 % / Redundancy: 11 % / Biso Wilson estimate: 12.39 Å2 / CC1/2: 1 / Net I/σ(I): 41.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 211 / CC1/2: 0.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LW1 Resolution: 1.5→45.44 Å / SU ML: 0.1282 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 26.0454
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→45.44 Å
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Refine LS restraints |
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LS refinement shell |
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