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Yorodumi- PDB-1opl: Structural basis for the auto-inhibition of c-Abl tyrosine kinase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1opl | ||||||
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Title | Structural basis for the auto-inhibition of c-Abl tyrosine kinase | ||||||
Components | proto-oncogene tyrosine-protein kinase | ||||||
Keywords | TRANSFERASE | ||||||
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 / 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 / BMP signaling pathway / Myogenesis / 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 / 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 / substrate adhesion-dependent cell spreading / SH2 domain binding / positive regulation of release of sequestered calcium ion into cytosol / post-embryonic development / thymus development / regulation of autophagy / neural tube closure / epidermal growth factor receptor signaling pathway / establishment of localization in cell / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 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 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1opl.cif.gz | 170.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1opl.ent.gz | 132.4 KB | Display | PDB format |
PDBx/mmJSON format | 1opl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1opl_validation.pdf.gz | 913 KB | Display | wwPDB validaton report |
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Full document | 1opl_full_validation.pdf.gz | 938.5 KB | Display | |
Data in XML | 1opl_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 1opl_validation.cif.gz | 41.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/1opl ftp://data.pdbj.org/pub/pdb/validation_reports/op/1opl | HTTPS FTP |
-Related structure data
Related structure data | 1opjC 1opkC 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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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.) Homo sapiens (human) / Gene: Abl / Plasmid: PFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00519, EC: 2.7.1.112 #2: Chemical | ChemComp-MYR / | #3: Chemical | |
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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: 2.68 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: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |