[English] 日本語
Yorodumi- PDB-4j9f: Crystal structure of the Abl-SH3 domain complexed with the high a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j9f | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Abl-SH3 domain complexed with the high affinity peptide P0 | ||||||
Components |
| ||||||
Keywords | Transferase/unknown function / beta shandwich / SH3 domain / kinase / poly proline rich motifs / Transferase / Transferase-unknown function complex | ||||||
Function / homology | Function and homology information regulation of actin filament depolymerization / negative regulation of small GTPase mediated signal transduction / semaphorin receptor binding / : / 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 ...regulation of actin filament depolymerization / negative regulation of small GTPase mediated signal transduction / semaphorin receptor binding / : / 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 / regulation of Rac protein signal transduction / neuroepithelial cell differentiation / ruffle assembly / 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 / regulation of blood vessel endothelial cell migration / 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 / cell junction assembly / filopodium assembly / activated T cell proliferation / establishment of epithelial cell apical/basal polarity / cellular response to dopamine / regulation of cell motility / regulation of Cdc42 protein signal transduction / proline-rich region binding / positive regulation of dendrite development / regulation of small GTPase mediated signal transduction / 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 / phagocytosis, engulfment / Fc-gamma receptor signaling pathway involved in phagocytosis / BMP signaling pathway / Myogenesis / cell leading edge / 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 / semaphorin-plexin signaling pathway / phagocytic cup / regulation of endocytosis / neuromuscular process controlling balance / actin monomer binding / negative regulation of long-term synaptic potentiation / endothelial cell migration / bicellular tight junction / 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 / RAC1 GTPase cycle / ERK1 and ERK2 cascade / positive regulation of interleukin-2 production / ephrin receptor binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.094 Å | ||||||
Authors | Camara-Artigas, A. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the Abl-SH3 domain complexed with the high affinity peptide P0 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4j9f.cif.gz | 126.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4j9f.ent.gz | 100.6 KB | Display | PDB format |
PDBx/mmJSON format | 4j9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j9f_validation.pdf.gz | 487.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4j9f_full_validation.pdf.gz | 490.2 KB | Display | |
Data in XML | 4j9f_validation.xml.gz | 13 KB | Display | |
Data in CIF | 4j9f_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/4j9f ftp://data.pdbj.org/pub/pdb/validation_reports/j9/4j9f | HTTPS FTP |
-Related structure data
Related structure data | 2o88S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
2 |
| |||||||||||||||
3 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
| |||||||||||||||
Details | biological unit is the complex between one molecule of SH3 domain and the peptide |
-Components
#1: Protein | Mass: 7009.694 Da / Num. of mol.: 3 / Fragment: SH3 domain (unp residues 60-121) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABL, ABL1, JTK7 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P00519, non-specific protein-tyrosine kinase #2: Protein/peptide | Mass: 1075.255 Da / Num. of mol.: 3 / Source method: obtained synthetically / References: UniProt: Q9Y3L3*PLUS #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.73 % |
---|---|
Crystal grow | Temperature: 298 K / pH: 7 Details: 2M Ammonium sulphate, 5% PEG300, 0.05M Litium Formate, 10 % glycerol, 0.1M MOPS , pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97 |
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: 1.094→74.85 Å / Num. obs: 77433 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 6.9 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.09→1.15 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.9 / % possible all: 94.9 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O88 Resolution: 1.094→21.84 Å / Occupancy max: 1 / Occupancy min: 0.1 / SU ML: 0.09 / σ(F): 0 / Phase error: 13.91 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.094→21.84 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|