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Yorodumi- PDB-1abq: CRYSTAL STRUCTURE OF THE UNLIGANDED ABL TYROSINE KINASE SH3 DOMAIN -
+Open data
-Basic information
Entry | Database: PDB / ID: 1abq | ||||||
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Title | CRYSTAL STRUCTURE OF THE UNLIGANDED ABL TYROSINE KINASE SH3 DOMAIN | ||||||
Components | ABL TYROSINE KINASE SRC-HOMOLOGY 3 (SH3) DOMAIN | ||||||
Keywords | KINASE / SH3 DOMAIN / TRANSFERASE (PHOSPHOTRANSFERASE) / PROTO-ONCOGENE | ||||||
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 / delta-catenin binding / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / Regulation of actin dynamics for phagocytic cup formation / 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 / alpha-beta T cell differentiation / syntaxin binding / 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 / B cell proliferation / regulation of microtubule polymerization / positive regulation of osteoblast proliferation / cell leading edge / 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 / 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 / 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 / neural tube closure / establishment of localization in cell / integrin-mediated signaling pathway / protein kinase C binding / regulation of actin cytoskeleton organization / 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 / cellular response to hydrogen peroxide / cell-cell adhesion Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Musacchio, A. / Wilmanns, M. / Saraste, M. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1994 Title: High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides. Authors: Musacchio, A. / Saraste, M. / Wilmanns, M. #1: Journal: Embo J. / Year: 1993 Title: Crystal Structure of the SH3 Domain in Human Fyn. Comparison of the Three-Dimensional Structures of the SH3 Domain in Tyrosine Kinases and Spectrin Authors: Noble, M.E.M. / Musacchio, A. / Courtneidge, S. / Saraste, M. / Wierenga, R. #2: Journal: Science / Year: 1993 Title: Identification of a Ten-Amino Acid SH3 Binding Site Authors: Ren, R. / Mayer, B. / Clark, K.L. / Baltimore, D. #3: Journal: Nature / Year: 1992 Title: Crystal Structure of a Src-Homology 3 (SH3) Domain Authors: Musacchio, A. / Noble, M.E.M. / Pauptit, R. / Wierenga, R. / Saraste, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1abq.cif.gz | 24.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1abq.ent.gz | 14 KB | Display | PDB format |
PDBx/mmJSON format | 1abq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/1abq ftp://data.pdbj.org/pub/pdb/validation_reports/ab/1abq | 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: 6880.580 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): PET / References: UniProt: P00520, EC: 2.7.1.112 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.73 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8.2 / Method: vapor diffusion, hanging drop / Details: used as seeds | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 Å |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 12, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | % possible obs: 96 % / Rmerge(I) obs: 0.08 |
Reflection | *PLUS Highest resolution: 2.8 Å / Rmerge(I) obs: 0.08 |
-Processing
Software |
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Refinement | Resolution: 2.8→8 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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