+Open data
-Basic information
Entry | Database: PDB / ID: 4a49 | |||||||||
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Title | Structure of phosphoTyr371-c-Cbl-UbcH5B complex | |||||||||
Components |
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Keywords | 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 / (E3-independent) E2 ubiquitin-conjugating enzyme / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / positive regulation of epidermal growth factor receptor signaling pathway / E2 ubiquitin-conjugating enzyme / Regulation of KIT 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 / (E3-independent) E2 ubiquitin-conjugating enzyme / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / positive regulation of epidermal growth factor receptor signaling pathway / E2 ubiquitin-conjugating enzyme / 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 / TGF-beta receptor signaling activates SMADs / response to starvation / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein autoubiquitination / protein K48-linked ubiquitination / ubiquitin ligase complex / FLT3 signaling by CBL mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / ephrin receptor binding / phosphotyrosine residue binding / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / cellular response to nerve growth factor stimulus / response to activity / Negative regulators of DDX58/IFIH1 signaling / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / response to gamma radiation / Peroxisomal protein import / Regulation of TNFR1 signaling / 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 / protein modification process / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Negative regulation of MET activity / Inactivation of CSF3 (G-CSF) signaling / receptor tyrosine kinase binding / CLEC7A (Dectin-1) signaling / cytokine-mediated signaling pathway / cilium / FCERI mediated NF-kB activation / positive regulation of receptor-mediated endocytosis / SH3 domain binding / protein polyubiquitination / ubiquitin-protein transferase activity / Signaling by CSF1 (M-CSF) in myeloid cells / male gonad development / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / E3 ubiquitin ligases ubiquitinate target proteins / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / Neddylation / 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 / ubiquitin protein ligase binding / DNA damage response / calcium ion binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / protein-containing complex / extracellular exosome / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.214 Å | |||||||||
Authors | Dou, H. / Buetow, L. / Hock, A. / Sibbet, G.J. / Vousden, K.H. / 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 | 4a49.cif.gz | 112.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a49.ent.gz | 87.6 KB | Display | PDB format |
PDBx/mmJSON format | 4a49.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a49_validation.pdf.gz | 435.2 KB | Display | wwPDB validaton report |
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Full document | 4a49_full_validation.pdf.gz | 435.9 KB | Display | |
Data in XML | 4a49_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 4a49_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/4a49 ftp://data.pdbj.org/pub/pdb/validation_reports/a4/4a49 | HTTPS FTP |
-Related structure data
Related structure data | 2y1mC 2y1nC 4a4bC 4a4cC 1fbvS 2eskS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9508.621 Da / Num. of mol.: 1 / Fragment: C-CBL RESIDUES 354-435 / Mutation: Y368F Source method: isolated from a genetically manipulated source Details: TYR371 IS PHOSPHORYLATED / Source: (gene. exp.) Homo sapiens (human) / Gene: CBL, CBL2, RNF55 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P22681, RING-type E3 ubiquitin transferase | ||||||||
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#2: Protein | Mass: 16755.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme | ||||||||
#3: Chemical | #4: Chemical | ChemComp-K / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | Y368 IS MUTATED TO PHE. Y371 IS PHOSPHORYL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67 % / Description: NONE |
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Crystal grow | Temperature: 291 K Details: 20% (W/V) PEG 3350 AND 0.2 M POTASSIUM THIOCYANATE AT 18 DEGREES CELSIUS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 19, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→40 Å / Num. obs: 20424 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 44.92 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.21→2.27 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2ESK AND 1FBV Resolution: 2.214→36.297 Å / SU ML: 0.57 / σ(F): 1.35 / Phase error: 19.67 / Stereochemistry target values: ML Details: CHAIN A RESIDUE 354-358 AND CHAIN B RESIDUE 1 ARE DISORDERED.
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.77 Å2 / ksol: 0.314 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.214→36.297 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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