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Yorodumi- PDB-1yvh: Crystal Structure of the c-Cbl TKB Domain in Complex with the APS... -
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-Basic information
Entry | Database: PDB / ID: 1yvh | ||||||
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Title | Crystal Structure of the c-Cbl TKB Domain in Complex with the APS pTyr-618 Phosphopeptide | ||||||
Components |
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Keywords | LIGASE / SIGNALING PROTEIN / IMMUNE SYSTEM / X-RAY CRYSTALLOGRAPHY / PHOSPHOTYROSINE / ADAPTER PROTEIN | ||||||
Function / homology | Function and homology information Regulation of KIT signaling / Factors involved in megakaryocyte development and platelet production / antigen receptor-mediated signaling pathway / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Ras protein signal transduction / regulation of Rap protein signal transduction / entry of bacterium into host cell / B-1 B cell homeostasis / flotillin complex ...Regulation of KIT signaling / Factors involved in megakaryocyte development and platelet production / antigen receptor-mediated signaling pathway / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Ras protein signal transduction / regulation of Rap protein signal transduction / entry of bacterium into host cell / B-1 B cell homeostasis / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / regulation of metabolic process / transmembrane receptor protein tyrosine kinase adaptor activity / 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 / cellular response to platelet-derived growth factor stimulus / response to starvation / protein monoubiquitination / TGF-beta receptor signaling activates SMADs / regulation of immune response / protein autoubiquitination / signaling adaptor activity / brown fat cell differentiation / stress fiber / FLT3 signaling by CBL mutants / ruffle / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / SH2 domain binding / phosphotyrosine residue binding / ephrin receptor binding / cellular response to nerve growth factor stimulus / InlB-mediated entry of Listeria monocytogenes into host cell / response to activity / actin filament / Regulation of signaling by CBL / response to gamma radiation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / EGFR downregulation / Negative regulation of FGFR1 signaling / B cell receptor signaling pathway / Spry regulation of FGF signaling / Constitutive Signaling by EGFRvIII / RING-type E3 ubiquitin transferase / cilium / Negative regulation of MET activity / receptor tyrosine kinase binding / SH3 domain binding / positive regulation of receptor-mediated endocytosis / protein polyubiquitination / cytokine-mediated signaling pathway / ubiquitin-protein transferase activity / male gonad development / Signaling by CSF1 (M-CSF) in myeloid cells / ubiquitin protein ligase activity / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / insulin receptor signaling pathway / Clathrin-mediated endocytosis / nervous system development / growth cone / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / actin cytoskeleton organization / response to ethanol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / intracellular signal transduction / 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 / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Hu, J. / Hubbard, S.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structural Characterization of a Novel Cbl Phosphotyrosine Recognition Motif in the APS Family of Adapter Proteins Authors: Hu, J. / Hubbard, S.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yvh.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yvh.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 1yvh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/1yvh ftp://data.pdbj.org/pub/pdb/validation_reports/yv/1yvh | HTTPS FTP |
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-Related structure data
Related structure data | 2cblS 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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Unit cell |
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-Components
#1: Protein | Mass: 38192.090 Da / Num. of mol.: 1 / Fragment: Tyrosine kinase binding domain, residues 25-351 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBL, CBL2, RNF55 / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P22681, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Protein/peptide | Mass: 1642.665 Da / Num. of mol.: 1 / Fragment: pTyr-618 phosphopeptide / Source method: obtained synthetically / Details: sequence appears in Rattus norvegicus, gene APS / References: UniProt: Q9Z200 |
#3: Chemical | ChemComp-MG / |
#4: 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: 3.1 Å3/Da / Density % sol: 59.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: PEG 8000, magnesium acetate, sodium cacodylate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 |
Detector | Detector: CCD / Date: Feb 17, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 29857 / Num. obs: 29857 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rsym value: 0.061 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CBL Resolution: 2.05→30 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 54.8 Å2 / ksol: 0.398 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→30 Å
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Refine LS restraints |
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