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Open data
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Basic information
Entry | Database: PDB / ID: 4a4c | ||||||
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Title | Structure of phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex | ||||||
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![]() | LIGASE/TRANSFERASE / LIGASE-TRANSFERASE COMPLEX | ||||||
Function / homology | ![]() T cell aggregation / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / T cell migration / regulation of Rap protein signal transduction / entry of bacterium into host cell / positive regulation of alpha-beta T cell proliferation / negative thymic T cell selection / (E3-independent) E2 ubiquitin-conjugating enzyme / flotillin complex ...T cell aggregation / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / T cell migration / regulation of Rap protein signal transduction / entry of bacterium into host cell / positive regulation of alpha-beta T cell proliferation / negative thymic T cell selection / (E3-independent) E2 ubiquitin-conjugating enzyme / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / beta selection / positive thymic T cell selection / positive regulation of alpha-beta T cell differentiation / positive regulation of T cell differentiation / positive regulation of epidermal growth factor receptor signaling pathway / T cell receptor complex / E2 ubiquitin-conjugating enzyme / Regulation of KIT signaling / mast cell degranulation / Interleukin-6 signaling / response to testosterone / B cell activation / cellular response to platelet-derived growth factor stimulus / negative regulation of epidermal growth factor receptor signaling pathway / Translocation of ZAP-70 to Immunological synapse / TGF-beta receptor signaling activates SMADs / response to starvation / protein monoubiquitination / ubiquitin conjugating enzyme activity / RHOH GTPase cycle / Generation of second messenger molecules / immunological synapse / T cell differentiation / protein autoubiquitination / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / positive regulation of calcium-mediated signaling / ubiquitin ligase complex / extrinsic component of cytoplasmic side of plasma membrane / FLT3 signaling by CBL mutants / cell surface receptor protein tyrosine kinase signaling pathway / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / T cell activation / 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 / calcium-mediated signaling / 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 / non-specific protein-tyrosine kinase / Spry regulation of FGF signaling / non-membrane spanning protein tyrosine kinase activity / 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 / peptidyl-tyrosine phosphorylation / protein polyubiquitination / ubiquitin-protein transferase activity / Signaling by CSF1 (M-CSF) in myeloid cells / male gonad development / ubiquitin protein ligase activity / cell-cell junction / 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 / T cell receptor signaling pathway / growth cone / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / protein tyrosine kinase activity / response to ethanol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dou, H. / Buetow, L. / Hock, A. / Sibbet, G.J. / Vousden, K.H. / Huang, D.T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 237.2 KB | Display | ![]() |
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PDB format | ![]() | 191.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.3 KB | Display | ![]() |
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Full document | ![]() | 464.3 KB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y1mC ![]() 2y1nC ![]() 4a49C ![]() 4a4bC ![]() 1fbvS ![]() 2eskS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AC
#1: Protein | Mass: 45152.805 Da / Num. of mol.: 1 Fragment: TKB DOMAIN, LINKER HELIX REGION, AND RING DOMAIN, RESIDUES 47-435 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P22681, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#3: Protein | Mass: 16755.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules B
#2: Protein/peptide | Mass: 1344.275 Da / Num. of mol.: 1 / Fragment: ZAP-70 PEPTIDE, RESIDUES 286-297 / Source method: obtained synthetically / Source: (synth.) ![]() References: UniProt: P43403, non-specific protein-tyrosine kinase |
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-Non-polymers , 3 types, 13 molecules ![](data/chem/img/ZN.gif)
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![](data/chem/img/HOH.gif)
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![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-CA / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | N-TERMINAL GS RESULTED FROM CLONING AND TEV CLEAVAGE. Y371 IS PHOSPHORYLATED. CORRESPONDS TO 286- ...N-TERMINAL GS RESULTED FROM CLONING AND TEV CLEAVAGE. Y371 IS PHOSPHORYL |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58 % / Description: NONE |
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Crystal grow | Temperature: 277 K Details: 50 MM HEPES, PH 7.5, 0.2 M KCL AND 31-35% (V/V) PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH) AT 4 DEGREES CELSIUS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 22290 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 16.8 % / Biso Wilson estimate: 84.14 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 4.2 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 2ESK, 1FBV Resolution: 2.704→29.325 Å / SU ML: 0.79 / σ(F): 1.35 / Phase error: 26.88 / Stereochemistry target values: ML Details: CHAIN A RESIDUE 47, CHAIN B, 1-3, CHAIN C RESIDUE 1 AND 129 ARE DISORDERED. FOLLOWING RESIDUES ARE BUILT AS ALA BECAUSE SIDE CHAIN DENSITY IS NOT VISIBLE. CHAIN A RESIDUES ...Details: CHAIN A RESIDUE 47, CHAIN B, 1-3, CHAIN C RESIDUE 1 AND 129 ARE DISORDERED. FOLLOWING RESIDUES ARE BUILT AS ALA BECAUSE SIDE CHAIN DENSITY IS NOT VISIBLE. CHAIN A RESIDUES 58,61,65,105,107,135,137, 191,192,322,354,358,359,361,362,364,365,366,367,369,379 AND CHAIN C RESIDUES 128,131,132,134,136,139,143.
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.117 Å2 / ksol: 0.302 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 101 Å2
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Refinement step | Cycle: LAST / Resolution: 2.704→29.325 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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