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Yorodumi- PDB-3buo: Crystal structure of c-Cbl-TKB domain complexed with its binding ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3buo | ||||||
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Title | Crystal structure of c-Cbl-TKB domain complexed with its binding motif in EGF receptor' | ||||||
Components |
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Keywords | LIGASE/SIGNALING PROTEIN / Cbl / TKB / ligase / signal transduction / proto-oncogene / complex / Anti-oncogene / ATP-binding / Cell cycle / Disease mutation / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Secreted / Transferase / Transmembrane / Tyrosine-protein kinase / Metal-binding / SH2 domain / Ubl conjugation pathway / 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 / entry of bacterium into host cell / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / entry of bacterium into host cell / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / response to UV-A / epidermal growth factor binding / positive regulation of epidermal growth factor receptor signaling pathway / PLCG1 events in ERBB2 signaling / tongue development / midgut development / ERBB2-EGFR signaling pathway / hydrogen peroxide metabolic process / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / regulation of nitric-oxide synthase activity / Regulation of KIT signaling / ERBB2 Activates PTK6 Signaling / morphogenesis of an epithelial fold / mast cell degranulation / intracellular vesicle / Signaling by EGFR / response to testosterone / Interleukin-6 signaling / response to cobalamin / negative regulation of epidermal growth factor receptor signaling pathway / response to starvation / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / cellular response to platelet-derived growth factor stimulus / Signaling by ERBB4 / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein insertion into membrane / eyelid development in camera-type eye / protein monoubiquitination / TGF-beta receptor signaling activates SMADs / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / regulation of JNK cascade / activation of phospholipase C activity / positive regulation of cyclin-dependent protein serine/threonine kinase activity / PI3K events in ERBB2 signaling / negative regulation of mitotic cell cycle / hair follicle development / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of G1/S transition of mitotic cell cycle / embryonic placenta development / positive regulation of bone resorption / GAB1 signalosome / protein autoubiquitination / positive regulation of nitric oxide mediated signal transduction / salivary gland morphogenesis / regulation of peptidyl-tyrosine phosphorylation / peptidyl-tyrosine autophosphorylation / positive regulation of glial cell proliferation / positive regulation of phosphorylation / positive regulation of vasoconstriction / FLT3 signaling by CBL mutants / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / cellular response to cadmium ion / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / positive regulation of DNA repair / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / GRB2 events in ERBB2 signaling / phosphotyrosine residue binding / transmembrane receptor protein tyrosine kinase activity / neurogenesis / ephrin receptor binding / cellular response to dexamethasone stimulus / SHC1 events in ERBB2 signaling / ossification / positive regulation of synaptic transmission, glutamatergic / basal plasma membrane / cellular response to nerve growth factor stimulus / regulation of ERK1 and ERK2 cascade / InlB-mediated entry of Listeria monocytogenes into host cell / neuron projection morphogenesis / positive regulation of superoxide anion generation / positive regulation of DNA replication / response to activity / Signal transduction by L1 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 | 3buo.cif.gz | 144.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3buo.ent.gz | 111.9 KB | Display | PDB format |
PDBx/mmJSON format | 3buo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/3buo ftp://data.pdbj.org/pub/pdb/validation_reports/bu/3buo | HTTPS FTP |
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-Related structure data
Related structure data | 3bumC 3bunC 3buwC 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 1553.502 Da / Num. of mol.: 2 / Fragment: UNP residues 1063-1075, pTyr-1069 phosphopeptide / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P00533 #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: 2.47 Å3/Da / Density % sol: 50.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.25M Na formate, 20% PEG 3350, pH 7.0, 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: Mar 25, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→40 Å / Num. obs: 21945 / % possible obs: 91.9 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.109 / Χ2: 1.228 / Net I/σ(I): 6.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 4066
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Solvent computation | Bsol: 11.576 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.644 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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Xplor file |
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