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Yorodumi- PDB-3eac: Crystal structure of SH2 domain of Human Csk (carboxyl-terminal s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eac | ||||||
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Title | Crystal structure of SH2 domain of Human Csk (carboxyl-terminal src kinase), Oxidized form. | ||||||
Components | Tyrosine-protein kinase CSK | ||||||
Keywords | TRANSFERASE / SH2 / CSK / DISULFIDE / OXIDIZED / Reduced / ATP-binding / Cell membrane / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / SH2 domain / SH3 domain / Tyrosine-protein kinase | ||||||
Function / homology | Function and homology information negative regulation of Golgi to plasma membrane protein transport / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of low-density lipoprotein particle clearance / proline-rich region binding / adherens junction organization / negative regulation of bone resorption / negative regulation of phagocytosis / cellular response to peptide hormone stimulus / GAB1 signalosome / Phosphorylation of CD3 and TCR zeta chains ...negative regulation of Golgi to plasma membrane protein transport / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of low-density lipoprotein particle clearance / proline-rich region binding / adherens junction organization / negative regulation of bone resorption / negative regulation of phagocytosis / cellular response to peptide hormone stimulus / GAB1 signalosome / Phosphorylation of CD3 and TCR zeta chains / oligodendrocyte differentiation / protein kinase A catalytic subunit binding / negative regulation of interleukin-6 production / RHOH GTPase cycle / PD-1 signaling / Negative regulation of FLT3 / T cell costimulation / Integrin signaling / protein tyrosine kinase binding / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / negative regulation of ERK1 and ERK2 cascade / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / cell-cell junction / T cell receptor signaling pathway / protein phosphatase binding / protein tyrosine kinase activity / adaptive immune response / protein phosphorylation / negative regulation of cell population proliferation / extracellular exosome / ATP binding / identical protein binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | ||||||
Authors | Liu, D. / Seidel, R.D. / Cowburn, D. | ||||||
Citation | Journal: Biophys Rep / Year: 2016 Title: Combining biophysical methods to analyze the disulfide bond in SH2 domain of C-terminal Src kinase. Authors: Liu, D. / Cowburn, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eac.cif.gz | 35.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eac.ent.gz | 23.2 KB | Display | PDB format |
PDBx/mmJSON format | 3eac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eac_validation.pdf.gz | 388.3 KB | Display | wwPDB validaton report |
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Full document | 3eac_full_validation.pdf.gz | 390.1 KB | Display | |
Data in XML | 3eac_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 3eac_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/3eac ftp://data.pdbj.org/pub/pdb/validation_reports/ea/3eac | HTTPS FTP |
-Related structure data
Related structure data | 3eazC 1k9aS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12162.913 Da / Num. of mol.: 1 / Fragment: SH2 Domain (UNP residues 73 to 178) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: BL21(DE3) / Gene: CSK / Plasmid: pTWIN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P41240, non-specific protein-tyrosine kinase |
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#2: 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: 1.83 Å3/Da / Density % sol: 32.67 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7.3 Details: 22% PEG 4000, 100 mM Bis-Tris, pH 7.3., EVAPORATION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 26, 2008 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.37→50 Å / Num. obs: 22360 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.9 % / Biso Wilson estimate: 10.284 Å2 |
Reflection shell | Highest resolution: 1.37 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K9A, sh2 part Resolution: 1.37→29.36 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.053 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.069 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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 mean: 11.359 Å2
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Refinement step | Cycle: LAST / Resolution: 1.37→29.36 Å
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LS refinement shell | Resolution: 1.37→1.405 Å / Total num. of bins used: 20
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