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Yorodumi- PDB-1opk: Structural basis for the auto-inhibition of c-Abl tyrosine kinase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1opk | ||||||
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Title | Structural basis for the auto-inhibition of c-Abl tyrosine kinase | ||||||
Components | Proto-oncogene tyrosine-protein kinase ABL1 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Cyclin D associated events in G1 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / circulatory system development / podocyte apoptotic process / DN4 thymocyte differentiation ...Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Cyclin D associated events in G1 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / circulatory system development / podocyte apoptotic process / DN4 thymocyte differentiation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / response to epinephrine / regulation of cellular senescence / transitional one stage B cell differentiation / regulation of modification of synaptic structure / Regulation of actin dynamics for phagocytic cup formation / 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 / regulation of extracellular matrix organization / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / neuropilin signaling pathway / neuropilin binding / Myogenesis / bubble DNA binding / activated T cell proliferation / regulation of Cdc42 protein signal transduction / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / myoblast proliferation / syntaxin binding / alpha-beta T cell differentiation / cardiac muscle cell proliferation / regulation of T cell differentiation / regulation of axon extension / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / cell leading edge / B cell proliferation / regulation of microtubule polymerization / positive regulation of osteoblast proliferation / platelet-derived growth factor receptor-beta signaling pathway / negative regulation of cellular senescence / positive regulation of focal adhesion assembly / associative learning / Bergmann glial cell differentiation / neuromuscular process controlling balance / platelet-derived growth factor receptor signaling pathway / negative regulation of BMP signaling pathway / negative regulation of mitotic cell cycle / negative regulation of long-term synaptic potentiation / endothelial cell migration / positive regulation of T cell migration / canonical NF-kappaB signal transduction / signal transduction in response to DNA damage / negative regulation of double-strand break repair via homologous recombination / BMP signaling pathway / phagocytosis / negative regulation of endothelial cell apoptotic process / four-way junction DNA binding / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of vasoconstriction / 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 / phosphotyrosine residue binding / response to endoplasmic reticulum stress / positive regulation of mitotic cell cycle / SH2 domain binding / substrate adhesion-dependent cell spreading / positive regulation of release of sequestered calcium ion into cytosol / post-embryonic development / thymus development / neural tube closure / establishment of localization in cell / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / neuron differentiation / epidermal growth factor receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / autophagy / cell-cell adhesion / SH3 domain binding / cellular response to hydrogen peroxide Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Nagar, B. / Hantschel, O. / Young, M.A. / Scheffzek, K. / Veach, D. / Bornmann, W. / Clarkson, B. / Superti-Furga, G. / Kuriyan, J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2003 Title: Structural basis for the autoinhibition of c-Abl tyrosine kinase Authors: Nagar, B. / Hantschel, O. / Young, M.A. / Scheffzek, K. / Veach, D. / Bornmann, W. / Clarkson, B. / Superti-Furga, G. / Kuriyan, J. #1: Journal: Cell(Cambridge,Mass.) / Year: 2003 Title: A myristoyl/phosphotyrosine switch regulates c-Abl Authors: Hantschel, O. / Nagar, B. / Guettler, S. / Kretzschmar, J. / Dorey, K. / Kuriyan, J. / Superti-Furga, G. | ||||||
History |
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Remark 999 | SEQUENCE Numbering of the residues corresponds to the sequence database numbering of the isoform IV ...SEQUENCE Numbering of the residues corresponds to the sequence database numbering of the isoform IV of the protein. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1opk.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1opk.ent.gz | 84.3 KB | Display | PDB format |
PDBx/mmJSON format | 1opk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1opk_validation.pdf.gz | 729.5 KB | Display | wwPDB validaton report |
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Full document | 1opk_full_validation.pdf.gz | 735.1 KB | Display | |
Data in XML | 1opk_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 1opk_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/1opk ftp://data.pdbj.org/pub/pdb/validation_reports/op/1opk | HTTPS FTP |
-Related structure data
Related structure data | 1opjC 1oplC 1m52S 2ablS C: citing same article (ref.) 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: 56189.164 Da / Num. of mol.: 1 / Fragment: SH3-SH2-kinase domain / Mutation: D382N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: ABL1 / Plasmid: PFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00520, EC: 2.7.1.112 |
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#2: Chemical | ChemComp-MYR / |
#3: Chemical | ChemComp-P16 / |
#4: Chemical | ChemComp-GOL / |
#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: 2.49 Å3/Da / Density % sol: 50.22 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 3350, 200 mM potassium nitrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 | |||||||||||||||||||||||||||||||||||||||||||||||||
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: ALS / Beamline: 8.2.2 / Wavelength: 1.0781 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2002 / Details: mirrors |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→38 Å / Num. all: 50963 / Num. obs: 50963 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.057 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 5078 / Rsym value: 0.584 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 38 Å / Num. measured all: 560273 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / % possible obs: 100 % / Rmerge(I) obs: 0.584 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1M52, 2ABL Resolution: 1.8→37.59 Å / Rfactor Rfree error: 0.004 / 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: 35.0282 Å2 / ksol: 0.366818 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→37.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 38 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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