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Yorodumi- PDB-3eg1: Crystal structure of the N114Q mutant of ABL-SH3 domain complexed... -
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-Basic information
Entry | Database: PDB / ID: 3eg1 | ||||||
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Title | Crystal structure of the N114Q mutant of ABL-SH3 domain complexed with a designed high-affinity peptide ligand: implications for SH3-ligand interactions | ||||||
Components |
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Keywords | Transferase/Signaling protein / beta / SH3 domain / ATP-binding / Cell adhesion / Cytoskeleton / Kinase / Lipoprotein / Magnesium / Manganese / Metal-binding / Myristate / Nucleotide-binding / Nucleus / Phosphoprotein / Proto-oncogene / SH2 domain / Transferase / Tyrosine-protein kinase / SIGNALING PROTEIN / Transferase-Signaling protein 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Camara-Artigas, A. | ||||||
Citation | 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. #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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eg1.cif.gz | 43.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eg1.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 3eg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eg1_validation.pdf.gz | 453.2 KB | Display | wwPDB validaton report |
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Full document | 3eg1_full_validation.pdf.gz | 454.4 KB | Display | |
Data in XML | 3eg1_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 3eg1_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/3eg1 ftp://data.pdbj.org/pub/pdb/validation_reports/eg/3eg1 | HTTPS FTP |
-Related structure data
Related structure data | 3eg0C 3eg2C 3eg3C 3eguC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 7023.720 Da / Num. of mol.: 2 / Fragment: SH3 DOMAIN, RESIDUES 60-121 / Mutation: N114Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: PBAT4 / Gene: ABL1, ABL, JTK7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P00519, non-specific protein-tyrosine kinase #2: Protein/peptide | Mass: 1035.149 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The author states that the p41 peptide is a member of a group of peptide ligands designed to bind specifically the Abl-SH3 domain. Source: (synth.) synthetic construct (others) #3: Chemical | #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: 1.89 Å3/Da / Density % sol: 34.98 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 2M ammonium sulphate, 0.4 M NaCl, 0.1 M sodium citrate, 10% glycerol, pH 3.5, vapor diffusion, hanging drop, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Dec 19, 2005 / Details: Montel Optics |
Radiation | Monochromator: BRUKER MICROSTAR MICRO-FOCUS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→47.636 Å / Num. all: 10944 / Num. obs: 10158 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 17.692 Å2 / Rmerge(I) obs: 0.0653 / Rsym value: 0.0653 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 1.26 % / Rmerge(I) obs: 0.2426 / Mean I/σ(I) obs: 3.49 / Num. unique all: 1123 / Rsym value: 0.2649 / % possible all: 72.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2o88 Resolution: 1.85→18 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 7.118 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.1 Å2 / Biso mean: 16.612 Å2 / Biso min: 4.49 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→18 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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