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Yorodumi- PDB-2etz: The NMR minimized average structure of the Itk SH2 domain bound t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2etz | ||||||
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Title | The NMR minimized average structure of the Itk SH2 domain bound to a phosphopeptide | ||||||
Components |
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Keywords | TRANSFERASE / cis/trans isomerization / interleukin-2 tyrosine kinase / Itk / t-cell specific kinase / tsk / src homology 2 / SH2 / proline / phosphotyrosine binding | ||||||
Function / homology | Function and homology information TCR signalosome / GPVI-mediated activation cascade / FCERI mediated MAPK activation / Generation of second messenger molecules / mast cell activation / FCERI mediated Ca+2 mobilization / gamma-delta T cell activation / NK T cell differentiation / DAP12 signaling / plasma membrane raft ...TCR signalosome / GPVI-mediated activation cascade / FCERI mediated MAPK activation / Generation of second messenger molecules / mast cell activation / FCERI mediated Ca+2 mobilization / gamma-delta T cell activation / NK T cell differentiation / DAP12 signaling / plasma membrane raft / activation of phospholipase C activity / positive regulation of cytokine production / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / cell-cell junction / T cell receptor signaling pathway / adaptive immune response / intracellular signal transduction / protein phosphorylation / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / Distance geometry simulated annealing was used for refinement | ||||||
Model type details | minimized average | ||||||
Authors | Sundd, M. / Pletneva, E.V. / Fulton, D.B. / Andreotti, A.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Molecular Details of Itk Activation by Prolyl Isomerization and Phospholigand Binding: The NMR Structure of the Itk SH2 Domain Bound to a Phosphopeptide. Authors: Pletneva, E.V. / Sundd, M. / Fulton, D.B. / Andreotti, A.H. #1: Journal: Nat.Struct.Biol. / Year: 2002 Title: Structural characterization of a proline-driven conformational switch within the Itk SH2 domain. Authors: Mallis, R.J. / Brazin, K.N. / Fulton, D.B. / Andreotti, A.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2etz.cif.gz | 50.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2etz.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 2etz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/2etz ftp://data.pdbj.org/pub/pdb/validation_reports/et/2etz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12560.243 Da / Num. of mol.: 1 / Fragment: SH2 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itk, Emt, Tlk, Tsk / Plasmid: pGEX(2T) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03526, EC: 2.7.1.112 |
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#2: Protein/peptide | Mass: 794.723 Da / Num. of mol.: 1 Fragment: phosphopeptide fragment sequence database residues 143-148 Source method: obtained synthetically Details: The sequence of the peptide is naturally found in Mus musculus (mouse). References: UniProt: Q60787 |
-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 conditions | Ionic strength: 125mM / pH: 7.4 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: Distance geometry simulated annealing was used for refinement Software ordinal: 1 Details: 2486 Intramolecular NOE restraints, 31 intermolecular NOE restraints, 63 dihedral angles calculated using HNHA experiment and TALOS and 27 hydrogen bonds (D20 exchange based restraints) | ||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: Average structure / Conformers calculated total number: 200 / Conformers submitted total number: 1 |