+Open data
-Basic information
Entry | Database: PDB / ID: 4a4c | ||||||
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Title | Structure of phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex | ||||||
Components |
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Keywords | LIGASE/TRANSFERASE / LIGASE-TRANSFERASE COMPLEX | ||||||
Function / homology | Function and homology information T cell aggregation / ubiquitin-dependent endocytosis / regulation of platelet-derived growth factor receptor-alpha signaling pathway / 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 / negative regulation of epidermal growth factor receptor signaling pathway ...T cell aggregation / ubiquitin-dependent endocytosis / regulation of platelet-derived growth factor receptor-alpha signaling pathway / 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 / negative regulation of epidermal growth factor receptor signaling pathway / 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 / Regulation of KIT signaling / E2 ubiquitin-conjugating enzyme / mast cell degranulation / Interleukin-6 signaling / response to testosterone / B cell activation / cellular response to platelet-derived growth factor stimulus / response to starvation / Translocation of ZAP-70 to Immunological synapse / protein monoubiquitination / TGF-beta receptor signaling activates SMADs / extrinsic component of cytoplasmic side of plasma membrane / ubiquitin conjugating enzyme activity / RHOH GTPase cycle / Generation of second messenger molecules / immunological synapse / T cell differentiation / protein K48-linked ubiquitination / protein autoubiquitination / Nuclear events stimulated by ALK signaling in cancer / ubiquitin ligase complex / cell surface receptor protein tyrosine kinase signaling pathway / FLT3 signaling by CBL mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / T cell activation / positive regulation of calcium-mediated signaling / ephrin receptor binding / phosphotyrosine residue binding / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / EGFR downregulation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / cellular response to nerve growth factor stimulus / Constitutive Signaling by EGFRvIII / response to activity / Negative regulators of DDX58/IFIH1 signaling / Regulation of signaling by CBL / response to gamma radiation / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / non-specific protein-tyrosine kinase / calcium-mediated signaling / Spry regulation of FGF signaling / non-membrane spanning protein tyrosine kinase activity / protein modification process / RING-type E3 ubiquitin transferase / peptidyl-tyrosine phosphorylation / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Negative regulation of MET activity / Inactivation of CSF3 (G-CSF) signaling / cilium / receptor tyrosine kinase binding / CLEC7A (Dectin-1) signaling / cytokine-mediated signaling pathway / FCERI mediated NF-kB activation / 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 / ubiquitin protein ligase activity / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / cell-cell junction / Clathrin-mediated endocytosis / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / cellular response to hypoxia / Neddylation / T cell receptor signaling pathway / protein tyrosine kinase activity / growth cone / ubiquitin-dependent protein catabolic process / response to ethanol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 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 | 4a4c.cif.gz | 237.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a4c.ent.gz | 191.3 KB | Display | PDB format |
PDBx/mmJSON format | 4a4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a4c_validation.pdf.gz | 453.3 KB | Display | wwPDB validaton report |
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Full document | 4a4c_full_validation.pdf.gz | 464.3 KB | Display | |
Data in XML | 4a4c_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 4a4c_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/4a4c ftp://data.pdbj.org/pub/pdb/validation_reports/a4/4a4c | HTTPS FTP |
-Related structure data
Related structure data | 2y1mC 2y1nC 4a49C 4a4bC 1fbvS 2eskS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD 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.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: P62837, ubiquitin-protein ligase |
-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.) HOMO SAPIENS (human) References: UniProt: P43403, non-specific protein-tyrosine kinase |
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-Non-polymers , 3 types, 13 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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