[English] 日本語
Yorodumi- PDB-7a34: Intertwined dimer of the c-Src SH3 domain mutant V111L-N113S-T114S -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a34 | ||||||
---|---|---|---|---|---|---|---|
Title | Intertwined dimer of the c-Src SH3 domain mutant V111L-N113S-T114S | ||||||
Components | Proto-oncogene tyrosine-protein kinase Src | ||||||
Keywords | PROTEIN BINDING / beta barrel / 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 / 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 / DCC mediated attractive signaling / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / 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 / regulation of cell cycle / endosome membrane / cell adhesion / innate immune response / signaling receptor binding / focal adhesion / 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: 1.85 Å | ||||||
Authors | Camara-Artigas, A. / Plaza-Garrido, M. / Salinas-Garcia, M.C. | ||||||
Funding support | Spain, 1items
| ||||||
Citation | Journal: To be published Title: Intertwined dimer of the c-Src SH3 domain mutant V111L-N113S-T114S Authors: Camara-Artigas, A. / Plaza-Garrido, M. / Salinas-Garcia, M.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7a34.cif.gz | 46.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7a34.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 7a34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/7a34 ftp://data.pdbj.org/pub/pdb/validation_reports/a3/7a34 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4jz3S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 6722.288 Da / Num. of mol.: 1 / Mutation: V111L N113S T114S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Plasmid: pHTP1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P00523, non-specific protein-tyrosine kinase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-PGE / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.99 % / Mosaicity: 0.12 ° |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 5% PEG300, 2M ammomium sulfate, 0.1M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→19.44 Å / Num. obs: 12766 / % possible obs: 99.5 % / Redundancy: 10.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.017 / Rrim(I) all: 0.056 / Net I/σ(I): 23.6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JZ3 Resolution: 1.85→19.44 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.07 / Phase error: 30.2 / 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 max: 84.93 Å2 / Biso mean: 44.3046 Å2 / Biso min: 22.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→19.44 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|