+Open data
-Basic information
Entry | Database: PDB / ID: 3egu | ||||||
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Title | Crystal structure of the N114A mutant of ABL-SH3 domain | ||||||
Components | Proto-oncogene tyrosine-protein kinase ABL1 | ||||||
Keywords | TRANSFERASE / beta / ATP-binding / Cell adhesion / Cytoskeleton / Kinase / Lipoprotein / Magnesium / Manganese / Metal-binding / Myristate / Nucleotide-binding / Nucleus / Phosphoprotein / Proto-oncogene / SH2 domain / SH3 domain / Tyrosine-protein kinase | ||||||
Function / homology | Function and homology information : / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / transitional one stage B cell differentiation ...: / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / transitional one stage B cell differentiation / activation of protein kinase C activity / nicotinate-nucleotide adenylyltransferase activity / regulation of modification of synaptic structure / positive regulation of microtubule binding / delta-catenin binding / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / mitochondrial depolarization / negative regulation of ubiquitin-protein transferase activity / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / negative regulation of protein serine/threonine kinase activity / activated T cell proliferation / cellular response to dopamine / regulation of cell motility / regulation of Cdc42 protein signal transduction / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / myoblast proliferation / alpha-beta T cell differentiation / regulation of hematopoietic stem cell differentiation / syntaxin binding / cardiac muscle cell proliferation / regulation of T cell differentiation / regulation of axon extension / HDR through Single Strand Annealing (SSA) / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / Fc-gamma receptor signaling pathway involved in phagocytosis / Myogenesis / regulation of microtubule polymerization / positive regulation of osteoblast proliferation / RUNX2 regulates osteoblast differentiation / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of focal adhesion assembly / negative regulation of cellular senescence / Bergmann glial cell differentiation / associative learning / neuromuscular process controlling balance / regulation of endocytosis / negative regulation of BMP signaling pathway / negative regulation of mitotic cell cycle / actin monomer binding / negative regulation of long-term synaptic potentiation / endothelial cell migration / RHO GTPases Activate WASPs and WAVEs / positive regulation of T cell migration / canonical NF-kappaB signal transduction / signal transduction in response to DNA damage / mismatch repair / negative regulation of double-strand break repair via homologous recombination / BMP signaling pathway / regulation of cell adhesion / negative regulation of endothelial cell apoptotic process / four-way junction DNA binding / positive regulation of substrate adhesion-dependent cell spreading / peptidyl-tyrosine autophosphorylation / positive regulation of vasoconstriction / positive regulation of stress fiber assembly / spleen development / ruffle / cellular response to transforming growth factor beta stimulus / positive regulation of establishment of T cell polarity / ERK1 and ERK2 cascade / positive regulation of interleukin-2 production / actin filament polymerization / phosphotyrosine residue binding / SH2 domain binding / response to endoplasmic reticulum stress / ephrin receptor binding / positive regulation of endothelial cell migration / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / positive regulation of release of sequestered calcium ion into cytosol / post-embryonic development / thymus development / regulation of autophagy / neural tube closure / establishment of localization in cell / integrin-mediated signaling pathway / protein kinase C binding / regulation of actin cytoskeleton organization Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.25 Å | ||||||
Authors | Camara-Artigas, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Role of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl. Authors: Palencia, A. / Camara-Artigas, A. / Pisabarro, M.T. / Martinez, J.C. / Luque, I. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: Crystallization by capillary counter-diffusion and structure determination of the N114A mutant of the SH3 domain of Abl tyrosine kinase complexed with a high-affinity peptide ligand Authors: Camara-Artigas, A. / Palencia, A. / Martinez, J.C. / Luque, I. / Gavira, J.A. / Garcia-Ruiz, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3egu.cif.gz | 25.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3egu.ent.gz | 15.5 KB | Display | PDB format |
PDBx/mmJSON format | 3egu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/3egu ftp://data.pdbj.org/pub/pdb/validation_reports/eg/3egu | 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: 6966.669 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN, RESIDUES 60-121 / Mutation: N114A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: PBAT4 / Gene: ABL1, ABL, JTK7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P00519, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-GOL / |
#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: 2.53 Å3/Da / Density % sol: 51.46 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2M ammonium sulphate, 5% PEG300, 10% glycerol, and 0.1 M of buffer solution, pH 7, vapor diffusion, hanging drop, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Feb 2, 2006 / Details: Montel Optics |
Radiation | Monochromator: BRUKER MICROSTAR MICRO-FOCUS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→44.47 Å / Num. all: 3938 / Num. obs: 3936 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.85 % / Biso Wilson estimate: 24.173 Å2 / Rmerge(I) obs: 0.0531 / Rsym value: 0.0531 |
Reflection shell | Resolution: 2.15→2.25 Å / Redundancy: 4.07 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 3.97 / Num. unique all: 491 / Rsym value: 0.303 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.25→13.61 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.903 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.721 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.297 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.09 Å2 / Biso mean: 20.071 Å2 / Biso min: 5.33 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→13.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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