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Yorodumi- PDB-3buw: Crystal structure of c-Cbl-TKB domain complexed with its binding ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3buw | ||||||
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Title | Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Syk | ||||||
Components |
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Keywords | LIGASE/SIGNALING PROTEIN / Cbl / TKB / ligase / signal transduction / proto-oncogene / complex / Alternative splicing / ATP-binding / Host-virus interaction / Kinase / Nucleotide-binding / Phosphoprotein / Polymorphism / SH2 domain / Transferase / Tyrosine-protein kinase / Ubl conjugation / Calcium / Cytoplasm / Metal-binding / Ubl conjugation pathway / Zinc / Zinc-finger / LIGASE-SIGNALING PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / serotonin secretion by platelet / interleukin-15 receptor binding / positive regulation of interleukin-3 production / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonic acid secretion / cellular response to lectin ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / serotonin secretion by platelet / interleukin-15 receptor binding / positive regulation of interleukin-3 production / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonic acid secretion / cellular response to lectin / gamma-delta T cell differentiation / positive regulation of gamma-delta T cell differentiation / B cell receptor complex / neutrophil activation involved in immune response / Toll-like receptor binding / regulation of platelet aggregation / positive regulation of alpha-beta T cell proliferation / leukocyte activation involved in immune response / entry of bacterium into host cell / positive regulation of mast cell cytokine production / regulation of platelet activation / lymph vessel development / flotillin complex / collagen-activated tyrosine kinase receptor signaling pathway / cell activation / positive regulation of mast cell degranulation / phosphatidylinositol 3-kinase regulatory subunit binding / macrophage activation involved in immune response / beta selection / regulation of phagocytosis / positive regulation of killing of cells of another organism / cellular response to molecule of fungal origin / regulation of tumor necrosis factor-mediated signaling pathway / leukotriene biosynthetic process / FLT3 signaling through SRC family kinases / early phagosome / positive regulation of monocyte chemotactic protein-1 production / interleukin-3-mediated signaling pathway / cellular response to lipid / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of cell adhesion mediated by integrin / regulation of DNA-binding transcription factor activity / Fc epsilon receptor (FCERI) signaling / Interleukin-2 signaling / positive regulation of alpha-beta T cell differentiation / blood vessel morphogenesis / T cell receptor complex / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of B cell differentiation / leukocyte cell-cell adhesion / Regulation of KIT signaling / mast cell degranulation / response to testosterone / Interleukin-6 signaling / Fc-gamma receptor signaling pathway involved in phagocytosis / negative regulation of epidermal growth factor receptor signaling pathway / response to starvation / cellular response to platelet-derived growth factor stimulus / Dectin-2 family / protein monoubiquitination / TGF-beta receptor signaling activates SMADs / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / phospholipase binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of interleukin-10 production / positive regulation of receptor internalization / cellular response to low-density lipoprotein particle stimulus / FCGR activation / positive regulation of type I interferon production / positive regulation of interleukin-4 production / positive regulation of bone resorption / phosphatase binding / Role of phospholipids in phagocytosis / protein autoubiquitination / Role of LAT2/NTAL/LAB on calcium mobilization / positive regulation of calcium-mediated signaling / Signaling by CSF3 (G-CSF) / negative regulation of inflammatory response to antigenic stimulus / FLT3 signaling by CBL mutants / GPVI-mediated activation cascade / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / positive regulation of TORC1 signaling / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of interleukin-12 production / SH2 domain binding / phosphotyrosine residue binding / ephrin receptor binding / Integrin signaling / FCERI mediated Ca+2 mobilization / cellular response to nerve growth factor stimulus / FCGR3A-mediated IL10 synthesis / regulation of ERK1 and ERK2 cascade / B cell differentiation / neutrophil chemotaxis / InlB-mediated entry of Listeria monocytogenes into host cell / positive regulation of superoxide anion generation / response to activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å | ||||||
Authors | Ng, C. / Jackson, R.A. / Buschdorf, J.P. / Sun, Q. / Guy, G.R. / Sivaraman, J. | ||||||
Citation | Journal: Embo J. / Year: 2008 Title: Structural basis for a novel intrapeptidyl H-bond and reverse binding of c-Cbl-TKB domain substrates Authors: Ng, C. / Jackson, R.A. / Buschdorf, J.P. / Sun, Q. / Guy, G.R. / Sivaraman, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3buw.cif.gz | 153.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3buw.ent.gz | 117.9 KB | Display | PDB format |
PDBx/mmJSON format | 3buw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/3buw ftp://data.pdbj.org/pub/pdb/validation_reports/bu/3buw | HTTPS FTP |
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-Related structure data
Related structure data | 3bumC 3bunC 3buoC 3buxC 2cblS 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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Unit cell |
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-Components
#1: Protein/peptide | Mass: 1543.565 Da / Num. of mol.: 2 / Fragment: UNP residues 317-329, pTyr-323 phosphopeptide / Source method: obtained synthetically / Details: synthetic construct / References: UniProt: P43405 #2: Protein | Mass: 38192.090 Da / Num. of mol.: 2 Fragment: c-Cbl TKB domain, CBL N-terminal, UNP residues 23-351 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBL, CBL2, RNF55 Plasmid details: Cas-Br-M (murine) ecotropic retroviral transforming sequence Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta References: UniProt: P22681, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #3: Water | ChemComp-HOH / | |
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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: 2.22 Å3/Da / Density % sol: 44.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.12M ammonium acetate, 18% PEG 3350, pH 6.5, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 27, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→40 Å / Num. obs: 113559 / % possible obs: 92.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.075 / Χ2: 0.767 / Net I/σ(I): 9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CBL Resolution: 1.45→20 Å / Cross valid method: THROUGHOUT / σ(F): 15493
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Solvent computation | Bsol: 46.214 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.012 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→20 Å
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Refine LS restraints |
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Xplor file |
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