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Yorodumi- PDB-3bun: Crystal structure of c-Cbl-TKB domain complexed with its binding ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bun | ||||||
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Title | Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Sprouty4 | ||||||
Components |
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Keywords | LIGASE/SIGNALING PROTEIN / Cbl / TKB / ligase / signal transduction / proto-oncogene / complex / Alternative splicing / Cytoplasm / Developmental protein / Membrane / Calcium / Metal-binding / Phosphoprotein / SH2 domain / Ubl conjugation pathway / Zinc / Zinc-finger / LIGASE-SIGNALING PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information animal organ development / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / negative regulation of fibroblast growth factor receptor signaling pathway / regulation of Rap protein signal transduction / entry of bacterium into host cell / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / negative regulation of Ras protein signal transduction / positive regulation of epidermal growth factor receptor signaling pathway ...animal organ development / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / negative regulation of fibroblast growth factor receptor signaling pathway / regulation of Rap protein signal transduction / entry of bacterium into host cell / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / negative regulation of Ras protein signal transduction / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / response to testosterone / Interleukin-6 signaling / negative regulation of epidermal growth factor receptor signaling pathway / response to starvation / cellular response to platelet-derived growth factor stimulus / TGF-beta receptor signaling activates SMADs / FLT3 signaling by CBL mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / phosphotyrosine residue binding / ephrin receptor binding / cellular response to nerve growth factor stimulus / negative regulation of MAP kinase activity / InlB-mediated entry of Listeria monocytogenes into host cell / response to activity / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / response to gamma radiation / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / EGFR downregulation / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / RING-type E3 ubiquitin transferase / Constitutive Signaling by EGFRvIII / cilium / Negative regulation of MET activity / negative regulation of ERK1 and ERK2 cascade / SH3 domain binding / cytokine-mediated signaling pathway / receptor tyrosine kinase binding / positive regulation of receptor-mediated endocytosis / ruffle membrane / ubiquitin-protein transferase activity / male gonad development / ubiquitin protein ligase activity / Signaling by CSF1 (M-CSF) in myeloid cells / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / ubiquitin-dependent protein catabolic process / growth cone / cellular response to hypoxia / response to ethanol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / cadherin binding / membrane raft / focal adhesion / DNA damage response / calcium ion binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 | 3bun.cif.gz | 87 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bun.ent.gz | 63.4 KB | Display | PDB format |
PDBx/mmJSON format | 3bun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/3bun ftp://data.pdbj.org/pub/pdb/validation_reports/bu/3bun | HTTPS FTP |
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-Related structure data
Related structure data | 3bumC 3buoC 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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3 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 1583.527 Da / Num. of mol.: 1 / Fragment: UNP residues 46-58, pTyr-53 phosphopeptide / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9C004 |
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#2: Protein | Mass: 38192.090 Da / Num. of mol.: 1 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M NA/K TARTRATE, 20% PEG 3350, pH 7.5, 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: Mar 25, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 31352 / % possible obs: 96.3 % / Redundancy: 18.1 % / Rmerge(I) obs: 0.052 / Χ2: 0.817 / Net I/σ(I): 12.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 47.686 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.99 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Xplor file |
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