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Yorodumi- PDB-5ih2: Structure, thermodynamics, and the role of conformational dynamic... -
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-Basic information
Entry | Database: PDB / ID: 5ih2 | ||||||
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Title | Structure, thermodynamics, and the role of conformational dynamics in the interactions between the N-terminal SH3 domain of CrkII and proline-rich motifs in cAbl | ||||||
Components |
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Keywords | SIGNALING PROTEIN / SH3 domain Polyproline II motif | ||||||
Function / homology | Function and homology information PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ARMS-mediated activation / MET activates RAP1 and RAC1 / MET receptor recycling / response to hepatocyte growth factor / cellular response to endothelin / Role of ABL in ROBO-SLIT signaling / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin ...PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ARMS-mediated activation / MET activates RAP1 and RAC1 / MET receptor recycling / response to hepatocyte growth factor / cellular response to endothelin / Role of ABL in ROBO-SLIT signaling / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / HDR through Single Strand Annealing (SSA) / regulation of leukocyte migration / response to peptide / Downstream signal transduction / regulation of intracellular signal transduction / postsynaptic specialization assembly / RHO GTPases Activate WASPs and WAVEs / protein phosphorylated amino acid binding / regulation of T cell migration / Cyclin D associated events in G1 / p130Cas linkage to MAPK signaling for integrins / reelin-mediated signaling pathway / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of dendrite development / transitional one stage B cell differentiation / 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 / positive regulation of skeletal muscle acetylcholine-gated channel clustering / regulation of cellular senescence / response to yeast / Regulation of signaling by CBL / regulation of modification of synaptic structure / regulation of Rac protein signal transduction / positive regulation of extracellular matrix organization / delta-catenin binding / B cell proliferation involved in immune response / Regulation of actin dynamics for phagocytic cup formation / neuroepithelial cell differentiation / negative regulation of wound healing / 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 / negative regulation of cell motility / neuropilin binding / bubble DNA binding / Myogenesis / regulation of Cdc42 protein signal transduction / activated T cell proliferation / VEGFA-VEGFR2 Pathway / protein localization to membrane / regulation of axon extension / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / myoblast proliferation / alpha-beta T cell differentiation / cellular response to insulin-like growth factor stimulus / syntaxin binding / negative regulation of natural killer cell mediated cytotoxicity / cardiac muscle cell proliferation / regulation of T cell differentiation / negative regulation of double-strand break repair via homologous recombination / establishment of cell polarity / positive regulation of cell migration involved in sprouting angiogenesis / regulation of GTPase activity / enzyme-linked receptor protein signaling pathway / negative regulation of cell-cell adhesion / dendrite development / regulation of microtubule polymerization / positive regulation of smooth muscle cell migration / B cell proliferation / positive regulation of osteoblast proliferation / cell leading edge / positive regulation of Rac protein signal transduction / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of focal adhesion assembly / negative regulation of cellular senescence / negative regulation of long-term synaptic potentiation / regulation of cell adhesion mediated by integrin / 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 / endothelial cell migration / cellular response to nitric oxide / ephrin receptor signaling pathway / regulation of signal transduction / positive regulation of T cell migration / canonical NF-kappaB signal transduction Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Endothia gyrosa (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Bhatt, V.S. / Zeng, D. / Krieger, I. / Sacchettini, J.C. / Cho, J.-H. | ||||||
Citation | Journal: Biophys.J. / Year: 2016 Title: Binding Mechanism of the N-Terminal SH3 Domain of CrkII and Proline-Rich Motifs in cAbl. Authors: Bhatt, V.S. / Zeng, D. / Krieger, I. / Sacchettini, J.C. / Cho, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ih2.cif.gz | 50.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ih2.ent.gz | 34 KB | Display | PDB format |
PDBx/mmJSON format | 5ih2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/5ih2 ftp://data.pdbj.org/pub/pdb/validation_reports/ih/5ih2 | HTTPS FTP |
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-Related structure data
Related structure data | 1ckaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABMN
#1: Protein | Mass: 6971.731 Da / Num. of mol.: 2 / Fragment: UNP residues 134-191 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crk, Crko / Production host: Escherichia coli (E. coli) / References: UniProt: Q64010 #2: Protein/peptide | Mass: 1285.561 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Endothia gyrosa (fungus) / References: UniProt: P00520*PLUS |
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-Non-polymers , 4 types, 188 molecules
#3: Chemical | ChemComp-PEG / | ||||
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#4: Chemical | ChemComp-NA / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 11478 / % possible obs: 99.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 38.055 |
Reflection shell | Resolution: 1.8→1.83 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1cka Resolution: 1.8→45.63 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.9 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.161 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.533 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→45.63 Å
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