+Open data
-Basic information
Entry | Database: PDB / ID: 2y1m | ||||||
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Title | Structure of native c-Cbl | ||||||
Components | E3 UBIQUITIN-PROTEIN LIGASE | ||||||
Keywords | LIGASE / UBIQUITIN RING E3 LIGASE | ||||||
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 / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / Interleukin-6 signaling ...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 / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / Interleukin-6 signaling / response to testosterone / cellular response to platelet-derived growth factor stimulus / negative regulation of epidermal growth factor receptor signaling pathway / response to starvation / TGF-beta receptor signaling activates SMADs / protein monoubiquitination / protein autoubiquitination / FLT3 signaling by CBL mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / phosphotyrosine residue binding / ephrin receptor binding / InlB-mediated entry of Listeria monocytogenes into host cell / cellular response to nerve growth factor stimulus / 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 / Constitutive Signaling by EGFRvIII / RING-type E3 ubiquitin transferase / Negative regulation of MET activity / cilium / receptor tyrosine kinase binding / cytokine-mediated signaling pathway / SH3 domain binding / positive regulation of receptor-mediated endocytosis / protein polyubiquitination / ubiquitin-protein transferase activity / Signaling by CSF1 (M-CSF) in myeloid cells / male gonad development / ubiquitin protein ligase activity / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / growth cone / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / 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 / Resolution: 2.67 Å | ||||||
Authors | Dou, H. / Sibbet, G.J. / Huang, D.T. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 Title: Structural Basis for Autoinhibition and Phosphorylation-Dependent Activation of C-Cbl. Authors: Dou, H. / Buetow, L. / Hock, A. / Sibbet, G.J. / Vousden, K.H. / Huang, D.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y1m.cif.gz | 461 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y1m.ent.gz | 379.9 KB | Display | PDB format |
PDBx/mmJSON format | 2y1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/2y1m ftp://data.pdbj.org/pub/pdb/validation_reports/y1/2y1m | HTTPS FTP |
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-Related structure data
Related structure data | 2y1nC 4a49C 4a4bC 4a4cC 1b47S 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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Unit cell |
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-Components
#1: Protein | Mass: 44928.695 Da / Num. of mol.: 6 / Fragment: RESIDUES 47-435 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P22681, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: 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: 3.52 Å3/Da / Density % sol: 65.04 % / Description: NONE |
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Crystal grow | pH: 9 Details: 0.1 M TRIS-HCL, PH 9.0-9.5, 3.7-4.0 M SODIUM FORMATE, 5 MM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9395 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 21, 2010 |
Radiation | Monochromator: SYNCHROTRON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→50 Å / Num. obs: 104817 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 49.02 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.67→2.81 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.4 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B47 Resolution: 2.67→47.615 Å / SU ML: 0.37 / σ(F): 0 / Phase error: 29.44 / Stereochemistry target values: ML Details: FOLLOWING RESIDUES WERE NOT BUILT DUE TO POORLY DEFINED ELECTRON DENSITY.CHAIN A RESIDUES 354-358 CHAIN B RESIDUES 356-359, CHAIN C RESIDUES 355-358, CHAIN D RESIDUES 355-358, CHAIN E ...Details: FOLLOWING RESIDUES WERE NOT BUILT DUE TO POORLY DEFINED ELECTRON DENSITY.CHAIN A RESIDUES 354-358 CHAIN B RESIDUES 356-359, CHAIN C RESIDUES 355-358, CHAIN D RESIDUES 355-358, CHAIN E RESIDUES 354-359 AND CHAIN F RESIDUES 354-358. GLU354 AND ASP359 IN CHAIN C WERE BUILT AS ALANINES DUE TO POORLY DEFINED ELECTRON DENSITY.
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.901 Å2 / ksol: 0.372 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.18 Å2
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Refinement step | Cycle: LAST / Resolution: 2.67→47.615 Å
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Refine LS restraints |
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LS refinement shell |
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