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Yorodumi- PDB-3bum: Crystal structure of c-Cbl-TKB domain complexed with its binding ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bum | ||||||
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Title | Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Sprouty2 | ||||||
Components |
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Keywords | LIGASE / signal transduction / proto-oncogene / complex / Cytoplasm / Developmental protein / Membrane / Microtubule / Polymorphism / Calcium / Metal-binding / Phosphoprotein / SH2 domain / Ubl conjugation pathway / Zinc / Zinc-finger | ||||||
Function / homology | Function and homology information microtubule end / lung growth / negative regulation of lens fiber cell differentiation / negative regulation of cell projection organization / ubiquitin-protein transferase inhibitor activity / negative regulation of neurotrophin TRK receptor signaling pathway / ubiquitin-dependent endocytosis / regulation of platelet-derived growth factor receptor-alpha signaling pathway / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of vascular endothelial growth factor signaling pathway ...microtubule end / lung growth / negative regulation of lens fiber cell differentiation / negative regulation of cell projection organization / ubiquitin-protein transferase inhibitor activity / negative regulation of neurotrophin TRK receptor signaling pathway / ubiquitin-dependent endocytosis / regulation of platelet-derived growth factor receptor-alpha signaling pathway / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of vascular endothelial growth factor signaling pathway / animal organ development / regulation of Rap protein signal transduction / bud elongation involved in lung branching / entry of bacterium into host cell / negative regulation of epidermal growth factor receptor signaling pathway / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / negative regulation of Ras protein signal transduction / protein serine/threonine kinase inhibitor activity / negative regulation of epithelial to mesenchymal transition / positive regulation of epidermal growth factor receptor signaling pathway / inner ear morphogenesis / Regulation of KIT signaling / cell fate commitment / mast cell degranulation / Interleukin-6 signaling / response to testosterone / cellular response to platelet-derived growth factor stimulus / negative regulation of peptidyl-threonine phosphorylation / response to starvation / protein monoubiquitination / TGF-beta receptor signaling activates SMADs / establishment of mitotic spindle orientation / cellular response to vascular endothelial growth factor stimulus / fibroblast growth factor receptor signaling pathway / protein autoubiquitination / negative regulation of angiogenesis / negative regulation of protein ubiquitination / FLT3 signaling by CBL mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / ERK1 and ERK2 cascade / ephrin receptor binding / phosphotyrosine residue binding / protein serine/threonine kinase activator activity / EGFR downregulation / InlB-mediated entry of Listeria monocytogenes into host cell / negative regulation of transforming growth factor beta receptor signaling pathway / cellular response to nerve growth factor stimulus / Constitutive Signaling by EGFRvIII / response to activity / cellular response to leukemia inhibitory factor / Regulation of signaling by CBL / response to gamma radiation / Negative regulation of FGFR3 signaling / sensory perception of sound / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / ruffle membrane / Spry regulation of FGF signaling / RING-type E3 ubiquitin transferase / Negative regulation of MET activity / cilium / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / cytokine-mediated signaling pathway / positive regulation of receptor-mediated endocytosis / SH3 domain binding / protein polyubiquitination / Signaling by CSF1 (M-CSF) in myeloid cells / ubiquitin-protein transferase activity / Cargo recognition for clathrin-mediated endocytosis / male gonad development / microtubule cytoskeleton / positive regulation of peptidyl-serine phosphorylation / ubiquitin protein ligase activity / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / actin cytoskeleton / cellular response to hypoxia / growth cone / ubiquitin-dependent protein catabolic process / response to ethanol / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / positive regulation of cell migration / protein ubiquitination / cadherin binding / membrane raft / negative regulation of cell population proliferation / focal adhesion / DNA damage response / calcium ion binding / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Ng, C. / Jackson, A.R. / Buschdorf, P.J. / Sun, Q. / Guy, R.G. / 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 | 3bum.cif.gz | 85.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bum.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 3bum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bum_validation.pdf.gz | 417.4 KB | Display | wwPDB validaton report |
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Full document | 3bum_full_validation.pdf.gz | 430.3 KB | Display | |
Data in XML | 3bum_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 3bum_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/3bum ftp://data.pdbj.org/pub/pdb/validation_reports/bu/3bum | HTTPS FTP |
-Related structure data
Related structure data | 3bunC 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: 1574.562 Da / Num. of mol.: 1 / Fragment: UNP residues 49-61 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPRY2 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: O43597 |
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#2: Protein | Mass: 38192.090 Da / Num. of mol.: 1 / Fragment: c-Cbl TKB domain, UNP residues 25-351 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBL, CBL2, RNF55 / 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: 2.97 Å3/Da / Density % sol: 58.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulfate, PEG3350, pH7.5, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Detector: CCD / Date: Sep 21, 2005 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.98→50 Å / Num. obs: 32750 / % possible obs: 99.9 % / Redundancy: 16.2 % / Rmerge(I) obs: 0.083 / Χ2: 1.162 / Net I/σ(I): 9.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2→20 Å / σ(F): 0
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Solvent computation | Bsol: 55.439 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.025 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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