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Yorodumi- PDB-1a81: CRYSTAL STRUCTURE OF THE TANDEM SH2 DOMAIN OF THE SYK KINASE BOUN... -
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-Basic information
Entry | Database: PDB / ID: 1a81 | ||||||
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Title | CRYSTAL STRUCTURE OF THE TANDEM SH2 DOMAIN OF THE SYK KINASE BOUND TO A DUALLY TYROSINE-PHOSPHORYLATED ITAM | ||||||
Components |
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Keywords | COMPLEX (TRANSFERASE/PEPTIDE) / COMPLEX (TRANSFERASE-PEPTIDE) / SYK / KINASE / SH2 DOMAIN / ITAM / COMPLEX (TRANSFERASE-PEPTIDE) complex | ||||||
Function / homology | Function and homology information gamma-delta T cell receptor complex / T cell anergy / interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / cellular response to lectin / gamma-delta T cell differentiation ...gamma-delta T cell receptor complex / T cell anergy / interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / cellular response to lectin / gamma-delta T cell differentiation / serotonin secretion by platelet / positive regulation of interleukin-3 production / positive regulation of gamma-delta T cell differentiation / B cell receptor complex / Toll-like receptor binding / regulation of platelet aggregation / positive regulation of alpha-beta T cell proliferation / leukocyte activation involved in immune response / neutrophil activation involved in immune response / CD4-positive, alpha-beta T cell proliferation / gamma-delta T cell activation / positive regulation of mast cell cytokine production / negative thymic T cell selection / positive regulation of mast cell degranulation / lymph vessel development / regulation of platelet activation / collagen-activated tyrosine kinase receptor signaling pathway / cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of killing of cells of another organism / alpha-beta T cell receptor complex / regulation of phagocytosis / beta selection / macrophage activation involved in immune response / positive thymic T cell selection / cellular response to molecule of fungal origin / early phagosome / FLT3 signaling through SRC family kinases / leukotriene biosynthetic process / regulation of tumor necrosis factor-mediated signaling pathway / signal complex assembly / positive regulation of monocyte chemotactic protein-1 production / interleukin-3-mediated signaling pathway / cellular response to lipid / regulation of DNA-binding transcription factor activity / positive regulation of cell adhesion mediated by integrin / Fc epsilon receptor (FCERI) signaling / Interleukin-2 signaling / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of alpha-beta T cell differentiation / blood vessel morphogenesis / positive regulation of cell-matrix adhesion / T cell receptor complex / positive regulation of B cell differentiation / leukocyte cell-cell adhesion / smoothened signaling pathway / mast cell degranulation / Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of interleukin-4 production / Dectin-2 family / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / dendrite development / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / phospholipase binding / positive regulation of receptor internalization / alpha-beta T cell activation / positive regulation of interleukin-10 production / cellular response to low-density lipoprotein particle stimulus / Generation of second messenger molecules / immunological synapse / FCGR activation / PD-1 signaling / positive regulation of type I interferon production / positive regulation of bone resorption / phosphatase binding / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / T cell receptor binding / negative regulation of smoothened signaling pathway / positive regulation of T cell proliferation / Signaling by CSF3 (G-CSF) / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of inflammatory response to antigenic stimulus / GPVI-mediated activation cascade / T cell costimulation / positive regulation of TORC1 signaling / T cell activation / positive regulation of interleukin-12 production / positive regulation of calcium-mediated signaling / positive regulation of interleukin-2 production / neutrophil chemotaxis / phosphotyrosine residue binding / Integrin signaling / FCERI mediated Ca+2 mobilization / SH2 domain binding / B cell differentiation / FCGR3A-mediated IL10 synthesis Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 Å | ||||||
Authors | Fuetterer, K. / Waksman, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Structural basis for Syk tyrosine kinase ubiquity in signal transduction pathways revealed by the crystal structure of its regulatory SH2 domains bound to a dually phosphorylated ITAM peptide. Authors: Futterer, K. / Wong, J. / Grucza, R.A. / Chan, A.C. / Waksman, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a81.cif.gz | 301.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a81.ent.gz | 254.7 KB | Display | PDB format |
PDBx/mmJSON format | 1a81.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/1a81 ftp://data.pdbj.org/pub/pdb/validation_reports/a8/1a81 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
-Components
#1: Protein | Mass: 28831.877 Da / Num. of mol.: 6 / Fragment: TANDEM SH2 DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SYK / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: P43405, EC: 2.7.1.112 #2: Protein/peptide | Mass: 2284.294 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P07766 |
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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: 3.05 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 10% (W/V) PEG800, 10% (V/V) PEG 200, 0.1M TRIS HCL PH 8.5 | ||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. obs: 40670 / % possible obs: 89.8 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rsym value: 0.051 |
Reflection shell | Resolution: 3→3.07 Å / Redundancy: 3 % / Rsym value: 0.139 / % possible all: 74.1 |
Reflection | *PLUS Num. measured all: 202021 / Rmerge(I) obs: 0.051 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 3→30 Å / Rfactor Rfree error: 0.015 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.14 Å / Total num. of bins used: 8
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