+Open data
-Basic information
Entry | Database: PDB / ID: 1g83 | ||||||
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Title | CRYSTAL STRUCTURE OF FYN SH3-SH2 | ||||||
Components | PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FYN | ||||||
Keywords | TRANSFERASE / BETA BARREL / ANTIPARALLEL BETA SHEET / ALPHA HELIX / 3-10 HELIX | ||||||
Function / homology | Function and homology information response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / growth factor receptor binding / regulation of glutamate receptor signaling pathway ...response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / growth factor receptor binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Platelet Adhesion to exposed collagen / CD28 co-stimulation / G protein-coupled glutamate receptor signaling pathway / positive regulation of protein localization to membrane / activated T cell proliferation / CRMPs in Sema3A signaling / positive regulation of cysteine-type endopeptidase activity / FLT3 signaling through SRC family kinases / negative regulation of dendritic spine maintenance / feeding behavior / type 5 metabotropic glutamate receptor binding / Nef and signal transduction / Nephrin family interactions / DCC mediated attractive signaling / EPH-Ephrin signaling / dendrite morphogenesis / CD28 dependent Vav1 pathway / Ephrin signaling / dendritic spine maintenance / Regulation of KIT signaling / tau-protein kinase activity / CTLA4 inhibitory signaling / phospholipase activator activity / leukocyte migration / Fc-gamma receptor signaling pathway involved in phagocytosis / EPHA-mediated growth cone collapse / cellular response to platelet-derived growth factor stimulus / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / phospholipase binding / response to amyloid-beta / glial cell projection / Sema3A PAK dependent Axon repulsion / FCGR activation / cellular response to glycine / alpha-tubulin binding / positive regulation of protein targeting to membrane / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / Role of LAT2/NTAL/LAB on calcium mobilization / vascular endothelial growth factor receptor signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of peptidyl-tyrosine phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / forebrain development / Signaling by ERBB2 / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of inflammatory response to antigenic stimulus / GPVI-mediated activation cascade / negative regulation of protein ubiquitination / cellular response to transforming growth factor beta stimulus / T cell costimulation / EPHB-mediated forward signaling / ephrin receptor binding / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / FCGR3A-mediated IL10 synthesis / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / learning / axon guidance / actin filament / Regulation of signaling by CBL / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / neuron migration / non-membrane spanning protein tyrosine kinase activity / modulation of chemical synaptic transmission / tau protein binding / protein catabolic process / Signaling by SCF-KIT / Schaffer collateral - CA1 synapse / negative regulation of protein catabolic process / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / cellular response to hydrogen peroxide / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / Signaling by CSF1 (M-CSF) in myeloid cells / Constitutive Signaling by Aberrant PI3K in Cancer / disordered domain specific binding / calcium ion transport / DAP12 signaling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Arold, S.T. / Ulmer, T.S. / Mulhern, T.D. / Werner, J.M. / Ladbury, J.E. / Campbell, I.D. / Noble, M.E.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: The role of the Src homology 3-Src homology 2 interface in the regulation of Src kinases. Authors: Arold, S.T. / Ulmer, T.S. / Mulhern, T.D. / Werner, J.M. / Ladbury, J.E. / Campbell, I.D. / Noble, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g83.cif.gz | 75 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g83.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 1g83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/1g83 ftp://data.pdbj.org/pub/pdb/validation_reports/g8/1g83 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18910.930 Da / Num. of mol.: 2 / Fragment: SH3 AND SH2 DOMAIN / Mutation: C238S, C239S, C245S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FYN / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P06241, 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: 2.81 Å3/Da / Density % sol: 56.19 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 6 Details: PEG 8000, sodium tartrate, TRIS , pH 6.0, VAPOR DIFFUSION, temperature 295.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9402 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 30, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9402 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→35.8 Å / Num. all: 10431 / Num. obs: 69967 / % possible obs: 82 % / Observed criterion σ(I): 0.9 / Redundancy: 2.1 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.074 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.309 / % possible all: 83.4 |
Reflection | *PLUS Num. obs: 10431 / % possible obs: 82 % / Num. measured all: 69967 / Rmerge(I) obs: 0.074 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→37 Å / σ(F): 0 / σ(I): 0
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Displacement parameters | Biso mean: 35 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.72 Å
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 37 Å / σ(F): 0 / Rfactor obs: 0.214 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 35 Å2 | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.6 Å / Rfactor Rfree: 0.361 / Rfactor Rwork: 0.318 |