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Yorodumi- PDB-4rtv: Crystal structure of the Src tyrosine kinase SH3 domain S94A/Q128... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rtv | ||||||
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Title | Crystal structure of the Src tyrosine kinase SH3 domain S94A/Q128R mutant in complex with the high affinity synthetic peptide APP12 | ||||||
Components |
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Keywords | PROTEIN BINDING / SIGNALING PROTEIN / beta shandwich / SH3 domain | ||||||
Function / homology | Function and homology information Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / CD28 co-stimulation / CTLA4 inhibitory signaling / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Recycling pathway of L1 / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RAF activation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / Downregulation of ERBB4 signaling / EPH-ephrin mediated repulsion of cells / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / Activated NTRK3 signals through PI3K / Downstream signal transduction / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / osteoclast development / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell junction / protein phosphatase binding / protein tyrosine kinase activity / mitochondrial inner membrane / cell differentiation / cytoskeleton / endosome membrane / regulation of cell cycle / cell adhesion / cell cycle / phosphorylation / signaling receptor binding / focal adhesion / innate immune response / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.37 Å | ||||||
Authors | Camara-Artigas, A. / Bacarizo, J. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the Src tyrosine kinase SH3 domain S94A/Q128R mutant in complex with the high affinity synthetic peptide APP12 Authors: Camara-Artigas, A. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rtv.cif.gz | 52.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rtv.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 4rtv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/4rtv ftp://data.pdbj.org/pub/pdb/validation_reports/rt/4rtv | HTTPS FTP |
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-Related structure data
Related structure data | 4jz4S S: Starting model for refinement |
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Similar 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: 6918.563 Da / Num. of mol.: 1 / Fragment: SH3 domain (UNP residues 85-141) / Mutation: S94A, Q128R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P00523, non-specific protein-tyrosine kinase |
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#2: Protein/peptide | Mass: 1412.705 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic high affinity peptide |
#3: 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: 33.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1M sodium acetate, 1.5M ammonium sulphate, 5% PEG 300, 10% Glycerol, pH 5.0, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979491 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2011 | |||||||||||||||||||||
Radiation | Monochromator: Channel-cut monochromator and a Kirkpatrick-Baez (KB) focusing system Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979491 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Redundancy: 9 % / Number: 123709 / Rmerge(I) obs: 0.047 / D res high: 1.37 Å / D res low: 35.57 Å / Num. obs: 13685 / % possible obs: 99.7 | |||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.37→35.57 Å / Num. all: 13726 / Num. obs: 13685 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 13.86 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 26.1 | |||||||||||||||||||||
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: 4JZ4 Resolution: 1.37→27.331 Å / SU ML: 0.12 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 17.26 / 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: 80.79 Å2 / Biso mean: 22.9008 Å2 / Biso min: 7.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→27.331 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: 9
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