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Yorodumi- PDB-2cbl: N-TERMINAL DOMAIN OF CBL IN COMPLEX WITH ITS BINDING SITE ON ZAP-70 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cbl | |||||||||
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Title | N-TERMINAL DOMAIN OF CBL IN COMPLEX WITH ITS BINDING SITE ON ZAP-70 | |||||||||
Components |
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Keywords | COMPLEX (PROTO-ONCOGENE/PEPTIDE) / PROTO-ONCOGENE / SIGNAL TRANSDUCTION / PHOSPHOTYROSINE BINDING / SH2 / COMPLEX (PROTO-ONCOGENE-PEPTIDE) / COMPLEX (PROTO-ONCOGENE-PEPTIDE) complex | |||||||||
Function / homology | Function and homology information 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 / positive regulation of alpha-beta T cell proliferation / entry of bacterium into host cell / negative thymic T cell selection / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding ...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 / positive regulation of alpha-beta T cell proliferation / entry of bacterium into host cell / negative thymic T cell selection / 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 / T cell receptor complex / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / Interleukin-6 signaling / response to testosterone / negative regulation of epidermal growth factor receptor signaling pathway / 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 / RHOH GTPase cycle / Generation of second messenger molecules / immunological synapse / T cell differentiation / protein autoubiquitination / positive regulation of calcium-mediated signaling / FLT3 signaling by CBL mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / extrinsic component of cytoplasmic side of plasma membrane / phosphotyrosine residue binding / ephrin receptor binding / T cell activation / InlB-mediated entry of Listeria monocytogenes into host cell / cellular response to nerve growth factor stimulus / response to activity / calcium-mediated signaling / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / response to gamma radiation / Negative regulation of FGFR2 signaling / EGFR downregulation / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Constitutive Signaling by EGFRvIII / RING-type E3 ubiquitin transferase / Negative regulation of MET activity / cilium / receptor tyrosine kinase binding / SH3 domain binding / protein polyubiquitination / cytokine-mediated signaling pathway / positive regulation of receptor-mediated endocytosis / peptidyl-tyrosine phosphorylation / ubiquitin-protein transferase activity / male gonad development / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / ubiquitin protein ligase activity / cell-cell junction / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / growth cone / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / T cell receptor signaling pathway / protein tyrosine kinase activity / response to ethanol / adaptive immune response / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / intracellular signal transduction / immune response / cadherin binding / membrane raft / protein phosphorylation / signaling receptor binding / focal adhesion / innate immune response / DNA damage response / calcium ion binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / ATP binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Meng, W. / Sawasdikosol, S. / Burakoff, S.J. / Eck, M.J. | |||||||||
Citation | Journal: Nature / Year: 1999 Title: Structure of the amino-terminal domain of Cbl complexed to its binding site on ZAP-70 kinase. Authors: Meng, W. / Sawasdikosol, S. / Burakoff, S.J. / Eck, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cbl.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cbl.ent.gz | 64.1 KB | Display | PDB format |
PDBx/mmJSON format | 2cbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/2cbl ftp://data.pdbj.org/pub/pdb/validation_reports/cb/2cbl | HTTPS FTP |
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-Related 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: 35429.961 Da / Num. of mol.: 1 / Fragment: DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: P22681 |
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#2: Protein/peptide | Mass: 1344.275 Da / Num. of mol.: 1 / Fragment: BINDING SITE FRAGMENT Source method: isolated from a genetically manipulated source References: UniProt: P43403*PLUS |
#3: Chemical | ChemComp-CA / |
#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: 3.18 Å3/Da / Density % sol: 61 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.1 / Details: pH 6.1 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 1, 1998 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→99 Å / Num. obs: 20620 / % possible obs: 76.9 % / Redundancy: 1.74 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 1 % / Rmerge(I) obs: 0.023 / Mean I/σ(I) obs: 1.5 / % possible all: 42.3 |
Reflection | *PLUS Num. measured all: 35952 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CBL-N Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 2.1
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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