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Yorodumi- PDB-4j9h: Crystal structure of the ABL-SH3 domain complexed with the design... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j9h | ||||||
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Title | Crystal structure of the ABL-SH3 domain complexed with the designed high-affinity peptide ligand P7 at pH 8 | ||||||
Components |
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Keywords | Transferase/unknown function / beta shandwich / SH3 domain / kinase / poly proline rich motifs / transferase / Transferase-unknown function complex | ||||||
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 / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Camara-Artigas, A. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the ABL-SH3 domain complexed with the designed high-affinity peptide ligand P7 Authors: Camara-Artigas, A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: Crystallization by capillary counter-diffusion and structure determination of the N114A mutant of the SH3 domain of Abl tyrosine kinase complexed with a high-affinity peptide ligand. Authors: Camara-Artigas, A. / Palencia, A. / Martinez, J.C. / Luque, I. / Gavira, J.A. / Garcia-Ruiz, J.M. #2: Journal: J.Biol.Chem. / Year: 2010 Title: Role of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl. Authors: Palencia, A. / Camara-Artigas, A. / Pisabarro, M.T. / Martinez, J.C. / Luque, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j9h.cif.gz | 237.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j9h.ent.gz | 194.9 KB | Display | PDB format |
PDBx/mmJSON format | 4j9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j9h_validation.pdf.gz | 488.1 KB | Display | wwPDB validaton report |
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Full document | 4j9h_full_validation.pdf.gz | 491.8 KB | Display | |
Data in XML | 4j9h_validation.xml.gz | 20 KB | Display | |
Data in CIF | 4j9h_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/4j9h ftp://data.pdbj.org/pub/pdb/validation_reports/j9/4j9h | HTTPS FTP |
-Related structure data
Related structure data | 4j9gC 2o88S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 7009.694 Da / Num. of mol.: 6 / Fragment: SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: PBAT4 / Gene: ABL, ABL1, JTK7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P00519, non-specific protein-tyrosine kinase #2: Protein/peptide | Mass: 1059.212 Da / Num. of mol.: 6 / Source method: obtained synthetically Details: This sequence has been optimized to increase the affinity #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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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: 2.02 Å3/Da / Density % sol: 39.16 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2M ammonium sulphate, 10% glicerol and 0.1 M Tris-HCl , pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2011 | |||||||||||||||||||||
Radiation | Monochromator: Channel cut ESRF monochromator and torodial focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.7→74.957 Å / Num. all: 41520 / Num. obs: 41520 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 10.76 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 18.2 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O88 Resolution: 1.7→19.522 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.21 / σ(F): 0 / σ(I): 0 / Phase error: 21.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.8 Å2 / Biso mean: 21.5558 Å2 / Biso min: 4.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→19.522 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29
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