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Yorodumi- PDB-2fo0: Organization of the SH3-SH2 Unit in Active and Inactive Forms of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fo0 | |||||||||
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Title | Organization of the SH3-SH2 Unit in Active and Inactive Forms of the c-Abl Tyrosine Kinase | |||||||||
Components | Proto-oncogene tyrosine-protein kinase ABL1 (1B ISOFORM) | |||||||||
Keywords | TRANSFERASE / N-terminal cap / autoinhibition / myristoylation / SH3-SH2 clamp / phosphoserine | |||||||||
Function / homology | Function and homology information signal transduction in response to DNA damage => GO:0042770 / circulatory system development => GO:0072359 / : / : / : / regulation of cell cycle => GO:0051726 / : / actin filament branching / : / : ...signal transduction in response to DNA damage => GO:0042770 / circulatory system development => GO:0072359 / : / : / : / regulation of cell cycle => GO:0051726 / : / actin filament branching / : / : / 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 / protein modification process => GO:0036211 / 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 / collateral sprouting / regulation of extracellular matrix organization / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / mitochondrial depolarization / neuropilin signaling pathway / negative regulation of ubiquitin-protein transferase activity / 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 / negative regulation of mitotic cell cycle / mitogen-activated protein kinase binding / myoblast proliferation / syntaxin binding / regulation of hematopoietic stem cell differentiation / negative regulation of BMP signaling pathway / alpha-beta T cell differentiation / 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 / positive regulation of muscle cell differentiation / BMP signaling pathway / Myogenesis / cell leading edge / positive regulation of osteoblast proliferation / regulation of microtubule polymerization / RUNX2 regulates osteoblast differentiation / platelet-derived growth factor receptor-beta signaling pathway / peptidyl-tyrosine autophosphorylation / negative regulation of cellular senescence / positive regulation of focal adhesion assembly / associative learning / Bergmann glial cell differentiation / positive regulation of vasoconstriction / regulation of endocytosis / neuromuscular process controlling balance / 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 / signal transduction in response to DNA damage / negative regulation of double-strand break repair via homologous recombination / regulation of cell adhesion / mismatch repair / negative regulation of endothelial cell apoptotic process / canonical NF-kappaB signal transduction / four-way junction DNA binding / positive regulation of substrate adhesion-dependent cell spreading / negative regulation of canonical NF-kappaB signal transduction / spleen development / positive regulation of stress fiber assembly / cellular response to transforming growth factor beta stimulus / ruffle / positive regulation of establishment of T cell polarity / ERK1 and ERK2 cascade / positive regulation of interleukin-2 production / ephrin receptor binding / actin filament polymerization Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | |||||||||
Authors | Nagar, B. / Hantschel, O. / Seeliger, M. / Davies, J.M. / Weis, W.I. / Superti-Furga, G. / Kuriyan, J. | |||||||||
Citation | Journal: Mol.Cell / Year: 2006 Title: Organization of the SH3-SH2 unit in active and inactive forms of the c-Abl tyrosine kinase. Authors: Nagar, B. / Hantschel, O. / Seeliger, M. / Davies, J.M. / Weis, W.I. / Superti-Furga, G. / Kuriyan, J. | |||||||||
History |
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Remark 999 | SEQUENCE Residues 15-56 of the original protein sequence were deleted. Myristoyl group (MYR) is ...SEQUENCE Residues 15-56 of the original protein sequence were deleted. Myristoyl group (MYR) is covalently attached to the N-terminus of the protein. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fo0.cif.gz | 114.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fo0.ent.gz | 84.6 KB | Display | PDB format |
PDBx/mmJSON format | 2fo0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fo0_validation.pdf.gz | 725.4 KB | Display | wwPDB validaton report |
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Full document | 2fo0_full_validation.pdf.gz | 732.7 KB | Display | |
Data in XML | 2fo0_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 2fo0_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/2fo0 ftp://data.pdbj.org/pub/pdb/validation_reports/fo/2fo0 | HTTPS FTP |
-Related structure data
Related structure data | 1opkS 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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Unit cell |
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-Components
#1: Protein | Mass: 56452.371 Da / Num. of mol.: 1 Fragment: Abl N-cap (residues 1-531, residues 15-56 deleted) Mutation: D382N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: c-Abl / Plasmid: PFASTBAC1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P00519-2, UniProt: P00519*PLUS, EC: 2.7.1.112 | ||
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#2: Chemical | ChemComp-MYR / | ||
#3: Chemical | ChemComp-P16 / | ||
#4: Chemical | #5: 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: 2.5 Å3/Da / Density % sol: 50.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 10000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 24, 2003 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→48.14 Å / Num. all: 25639 / Num. obs: 25639 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.095 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.27→2.35 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2026 / Rsym value: 0.289 / % possible all: 76.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OPK Resolution: 2.27→48.14 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 318702.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.6955 Å2 / ksol: 0.376791 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.27→48.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.27→2.41 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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