+Open data
-Basic information
Entry | Database: PDB / ID: 1yi6 | ||||||
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Title | C-term tail segment of human tyrosine kinase (258-533) | ||||||
Components | Proto-oncogene tyrosine-protein kinase Src | ||||||
Keywords | TRANSFERASE / SRC / TYROSINE KINASE / PHOSPHORYLATION / REGULATION / SH2 / SH3 | ||||||
Function / homology | Function and homology information regulation of toll-like receptor 3 signaling pathway / positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / cellular response to prolactin / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly ...regulation of toll-like receptor 3 signaling pathway / positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / cellular response to prolactin / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly / regulation of cell-cell adhesion / positive regulation of dephosphorylation / response to mineralocorticoid / Regulation of commissural axon pathfinding by SLIT and ROBO / ERBB2 signaling pathway / regulation of epithelial cell migration / positive regulation of protein transport / Regulation of gap junction activity / regulation of vascular permeability / entry of bacterium into host cell / BMP receptor binding / positive regulation of lamellipodium morphogenesis / cellular response to progesterone stimulus / positive regulation of integrin activation / Activated NTRK2 signals through FYN / negative regulation of focal adhesion assembly / skeletal muscle cell proliferation / positive regulation of protein processing / negative regulation of telomerase activity / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / CD28 co-stimulation / positive regulation of glucose metabolic process / transcytosis / Activated NTRK3 signals through PI3K / connexin binding / cellular response to fluid shear stress / focal adhesion assembly / signal complex assembly / response to acidic pH / podosome / positive regulation of small GTPase mediated signal transduction / positive regulation of Ras protein signal transduction / positive regulation of podosome assembly / Regulation of RUNX1 Expression and Activity / regulation of bone resorption / branching involved in mammary gland duct morphogenesis / DCC mediated attractive signaling / negative regulation of mitochondrial depolarization / adherens junction organization / osteoclast development / myoblast proliferation / EPH-Ephrin signaling / Ephrin signaling / odontogenesis / cellular response to peptide hormone stimulus / Signal regulatory protein family interactions / cellular response to fatty acid / MET activates PTK2 signaling / regulation of early endosome to late endosome transport / oogenesis / Receptor Mediated Mitophagy / GP1b-IX-V activation signalling / Regulation of KIT signaling / Signaling by ALK / postsynaptic specialization, intracellular component / CTLA4 inhibitory signaling / Signaling by EGFR / phospholipase activator activity / leukocyte migration / DNA biosynthetic process / EPHA-mediated growth cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / interleukin-6-mediated signaling pathway / p130Cas linkage to MAPK signaling for integrins / negative regulation of hippo signaling / positive regulation of epithelial cell migration / positive regulation of Notch signaling pathway / stress fiber assembly / cellular response to platelet-derived growth factor stimulus / positive regulation of smooth muscle cell migration / regulation of heart rate by cardiac conduction / Recycling pathway of L1 / RUNX2 regulates osteoblast differentiation / progesterone receptor signaling pathway / dendritic growth cone / stimulatory C-type lectin receptor signaling pathway / negative regulation of telomere maintenance via telomerase / uterus development / PECAM1 interactions / phospholipase binding / neurotrophin TRK receptor signaling pathway / Long-term potentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / FCGR activation / EPH-ephrin mediated repulsion of cells / negative regulation of anoikis Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Fleury, D. / Sarubbi, E. / Courjaud, A. / Guitton, J.D. / Ducruix, A. | ||||||
Citation | Journal: To be published Title: Structure of the unphosphorylated C-terminal tail segment of the SRC kinase and its role in SRC activity regulation Authors: Fleury, D. / Sarubbi, E. / Courjaud, A. / Guitton, J.D. / Ducruix, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yi6.cif.gz | 133.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yi6.ent.gz | 104.4 KB | Display | PDB format |
PDBx/mmJSON format | 1yi6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/1yi6 ftp://data.pdbj.org/pub/pdb/validation_reports/yi/1yi6 | HTTPS FTP |
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-Related structure data
Related structure data | 2srcS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31816.316 Da / Num. of mol.: 2 / Fragment: residues 258-533 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12931, EC: 2.7.1.112 #2: Water | ChemComp-HOH / | |
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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: 2.41 Å3/Da / Density % sol: 50.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Sep 21, 2000 |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.97 Å / Num. all: 39386 / Num. obs: 37400 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.2 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.069 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3910 / Rsym value: 0.205 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2src Resolution: 2→19 Å / σ(F): 1 / σ(I): 4 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 16.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
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