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- PDB-1opl: Structural basis for the auto-inhibition of c-Abl tyrosine kinase -
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Open data
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Basic information
Entry | Database: PDB / ID: 1opl | ||||||
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Title | Structural basis for the auto-inhibition of c-Abl tyrosine kinase | ||||||
![]() | proto-oncogene tyrosine-protein kinase | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() : / 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 / regulation of hematopoietic stem cell differentiation / syntaxin binding / 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 / Myogenesis / regulation of microtubule polymerization / positive regulation of osteoblast proliferation / RUNX2 regulates osteoblast differentiation / 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 / regulation of endocytosis / negative regulation of BMP signaling pathway / negative regulation of mitotic cell cycle / negative regulation of long-term synaptic potentiation / actin monomer binding / 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 / negative regulation of double-strand break repair via homologous recombination / regulation of cell adhesion / BMP signaling pathway / mismatch repair / negative regulation of endothelial cell apoptotic process / four-way junction DNA binding / peptidyl-tyrosine autophosphorylation / 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 / positive regulation of endothelial cell migration / 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 / regulation of autophagy / neural tube closure / establishment of localization in cell / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nagar, B. / Hantschel, O. / Young, M.A. / Scheffzek, K. / Veach, D. / Bornmann, W. / Clarkson, B. / Superti-Furga, G. / Kuriyan, J. | ||||||
![]() | ![]() 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: ![]() 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 The bound myristoyl group is from the naturally occurring N-terminal myristoyl ...SEQUENCE The bound myristoyl group is from the naturally occurring N-terminal myristoyl modification that is connected to the SH3 domain of the protein chain A by 79 residues that could not be modeled. An O atom has been intentionally omitted from MYR since the O atom is not chemically present in a myristoyl group that is attached to the protein. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.4 KB | Display | ![]() |
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PDB format | ![]() | 132.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 913 KB | Display | ![]() |
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Full document | ![]() | 938.5 KB | Display | |
Data in XML | ![]() | 30.7 KB | Display | |
Data in CIF | ![]() | 41.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1opjC ![]() 1opkC ![]() 1m52S ![]() 2ablS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 61019.672 Da / Num. of mol.: 2 Fragment: N-terminal 531 residues (MYR-SH3-SH2-Kinase domain) Mutation: D382N, K29R, E29D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MYR / | #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.13 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.8 M ammonium tartrate , 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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 13, 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 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→75 Å / Num. all: 17250 / Num. obs: 17250 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 84.8 Å2 / Rsym value: 0.081 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 3.4→3.52 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 1617 / Rsym value: 0.465 / % possible all: 91.4 |
Reflection | *PLUS Lowest resolution: 75 Å / Num. measured all: 105428 / Rmerge(I) obs: 0.081 |
Reflection shell | *PLUS Highest resolution: 3.4 Å / % possible obs: 91.4 % / Rmerge(I) obs: 0.465 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1M52, 2ABL Resolution: 3.42→29.95 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The structure was refined by superimposing the refined high resolution structure of c-Abl (pdb entry 1OPK) on the molecular replacement solution and optimizing positions of individual ...Details: The structure was refined by superimposing the refined high resolution structure of c-Abl (pdb entry 1OPK) on the molecular replacement solution and optimizing positions of individual domains by rigid-body refinement. Following this, only overall domain B-factors were applied to molecule B, whereas individual B-factors were refined for molecule A.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.717 Å2 / ksol: 0.277405 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 123.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.42→29.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.61 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.4 Å / Lowest resolution: 75 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 3.4 Å / Lowest resolution: 3.52 Å |