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Yorodumi- PDB-2rsy: Solution structure of the SH2 domain of Csk in complex with a pho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rsy | ||||||
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Title | Solution structure of the SH2 domain of Csk in complex with a phosphopeptide from Cbp | ||||||
Components |
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Keywords | TRANSFERASE/SIGNALING PROTEIN / SH2 domain / Csk / Cbp / solution structure / TRANSFERASE-SIGNALING PROTEIN complex | ||||||
Function / homology | Function and homology information GAB1 signalosome / PD-1 signaling / Phosphorylation of CD3 and TCR zeta chains / Integrin signaling / : / negative regulation of Golgi to plasma membrane protein transport / RHOH GTPase cycle / regulation of Fc receptor mediated stimulatory signaling pathway / MAP2K and MAPK activation / negative regulation of T cell activation ...GAB1 signalosome / PD-1 signaling / Phosphorylation of CD3 and TCR zeta chains / Integrin signaling / : / negative regulation of Golgi to plasma membrane protein transport / RHOH GTPase cycle / regulation of Fc receptor mediated stimulatory signaling pathway / MAP2K and MAPK activation / negative regulation of T cell activation / negative regulation of low-density lipoprotein particle clearance / transmembrane receptor protein tyrosine kinase adaptor activity / proline-rich region binding / negative regulation of phagocytosis / negative regulation of bone resorption / adherens junction organization / regulation of T cell activation / cellular response to peptide hormone stimulus / oligodendrocyte differentiation / plasma membrane => GO:0005886 / protein kinase A catalytic subunit binding / negative regulation of interleukin-6 production / SH2 domain binding / protein tyrosine kinase binding / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / negative regulation of ERK1 and ERK2 cascade / cell-cell junction / protein phosphatase binding / protein tyrosine kinase activity / adaptive immune response / intracellular signal transduction / membrane raft / negative regulation of cell population proliferation / phosphorylation / signal transduction / ATP binding / identical protein binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Model details | target function, model1 | ||||||
Authors | Tanaka, H. / Akagi, K. / Oneyama, C. / Tanaka, M. / Sasaki, Y. / Kanou, T. / Lee, Y. / Yokogawa, D. / Debenecker, M. / Nakagawa, A. ...Tanaka, H. / Akagi, K. / Oneyama, C. / Tanaka, M. / Sasaki, Y. / Kanou, T. / Lee, Y. / Yokogawa, D. / Debenecker, M. / Nakagawa, A. / Okada, M. / Ikegami, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Identification of a new interaction mode between the Src homology 2 domain of C-terminal Src kinase (Csk) and Csk-binding protein/phosphoprotein associated with glycosphingolipid microdomains. Authors: Tanaka, H. / Akagi, K. / Oneyama, C. / Tanaka, M. / Sasaki, Y. / Kanou, T. / Lee, Y.H. / Yokogawa, D. / Dobenecker, M.W. / Nakagawa, A. / Okada, M. / Ikegami, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rsy.cif.gz | 963.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rsy.ent.gz | 850.4 KB | Display | PDB format |
PDBx/mmJSON format | 2rsy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/2rsy ftp://data.pdbj.org/pub/pdb/validation_reports/rs/2rsy | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11473.135 Da / Num. of mol.: 1 / Fragment: Src homology 2 domain, UNP residues 80-173 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Csk / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) References: UniProt: P32577, non-specific protein-tyrosine kinase |
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#2: Protein/peptide | Mass: 4263.566 Da / Num. of mol.: 1 / Fragment: Cbp, UNP residues 288-321 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pag1, Cbp, Pag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9JM80 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.076 / pH: 6.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 2935 / NOE intraresidue total count: 604 / NOE long range total count: 1000 / NOE medium range total count: 552 / NOE sequential total count: 779 | ||||||||||||||||||||||||||||||
NMR representative | Selection criteria: target function | ||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1 | ||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.0043 Å / Distance rms dev error: 0.0005 Å |