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- PDB-3buo: Crystal structure of c-Cbl-TKB domain complexed with its binding ... -
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Open data
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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' | ||||||
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![]() | 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 | ![]() 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 / PLCG1 events in ERBB2 signaling / tongue development / positive regulation of epidermal growth factor receptor signaling pathway / midgut development / ERBB2-EGFR signaling pathway / hydrogen peroxide metabolic process / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / Regulation of KIT signaling / mast cell degranulation / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / intracellular vesicle / Interleukin-6 signaling / response to testosterone / Signaling by EGFR / cellular response to platelet-derived growth factor stimulus / response to cobalamin / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / negative regulation of epidermal growth factor receptor signaling pathway / Signaling by ERBB4 / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / eyelid development in camera-type eye / protein insertion into membrane / TGF-beta receptor signaling activates SMADs / cerebral cortex cell migration / response to starvation / protein monoubiquitination / ERBB2 Regulates Cell Motility / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / : / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of mitotic cell cycle / hair follicle development / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / MAP kinase kinase kinase activity / embryonic placenta development / positive regulation of bone resorption / positive regulation of G1/S transition of mitotic cell cycle / GAB1 signalosome / protein autoubiquitination / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / regulation of peptidyl-tyrosine phosphorylation / positive regulation of phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / FLT3 signaling by CBL mutants / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / cellular response to cadmium ion / positive regulation of DNA repair / EGFR Transactivation by Gastrin / GRB2 events in ERBB2 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ephrin receptor binding / phosphotyrosine residue binding / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / positive regulation of synaptic transmission, glutamatergic / ossification / cellular response to dexamethasone stimulus / basal plasma membrane / neurogenesis / regulation of ERK1 and ERK2 cascade / InlB-mediated entry of Listeria monocytogenes into host cell / neuron projection morphogenesis / cellular response to nerve growth factor stimulus / positive regulation of superoxide anion generation / positive regulation of DNA replication / epithelial cell proliferation / response to activity / Signal transduction by L1 Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Ng, C. / Jackson, R.A. / Buschdorf, J.P. / Sun, Q. / Guy, G.R. / Sivaraman, J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.8 KB | Display | ![]() |
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PDB format | ![]() | 111.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.5 KB | Display | ![]() |
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Full document | ![]() | 497.4 KB | Display | |
Data in XML | ![]() | 32.3 KB | Display | |
Data in CIF | ![]() | 45 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bumC ![]() 3bunC ![]() 3buwC ![]() 3buxC ![]() 2cblS 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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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.) ![]() #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.) ![]() Plasmid details: Cas-Br-M (murine) ecotropic retroviral transforming sequence Plasmid: pGEX4T1 / Production host: ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() 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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