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Yorodumi- PDB-2yu7: Solution structure of the SHP-1 C-terminal SH2 domain complexed w... -
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-Basic information
Entry | Database: PDB / ID: 2yu7 | ||||||
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Title | Solution structure of the SHP-1 C-terminal SH2 domain complexed with a tyrosine-phosphorylated peptide from NKG2A | ||||||
Components |
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Keywords | SIGNALING PROTEIN / SH2 domain / Protein-peptide complex / Phosphorylated peptide recognition / Phosphotyrosine binding domain / Signal Transduction / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information inhibitory MHC class Ib receptor activity / CD8-positive, gamma-delta intraepithelial T cell differentiation / HLA-E specific inhibitory MHC class Ib receptor activity / natural killer cell inhibitory signaling pathway / negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / MHC class I protein complex binding / regulation of B cell differentiation / regulation of natural killer cell activation / negative regulation of peptidyl-tyrosine phosphorylation ...inhibitory MHC class Ib receptor activity / CD8-positive, gamma-delta intraepithelial T cell differentiation / HLA-E specific inhibitory MHC class Ib receptor activity / natural killer cell inhibitory signaling pathway / negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / MHC class I protein complex binding / regulation of B cell differentiation / regulation of natural killer cell activation / negative regulation of peptidyl-tyrosine phosphorylation / epididymis development / negative regulation of T cell mediated cytotoxicity / phosphorylation-dependent protein binding / negative regulation of inflammatory response to wounding / transmembrane receptor protein tyrosine phosphatase activity / natural killer cell mediated cytotoxicity / alpha-beta T cell receptor complex / regulation of release of sequestered calcium ion into cytosol / CD22 mediated BCR regulation / Interleukin-37 signaling / positive regulation of cell adhesion mediated by integrin / Costimulation by the CD28 family / negative regulation of natural killer cell mediated cytotoxicity / Signal regulatory protein family interactions / platelet formation / megakaryocyte development / negative regulation of T cell receptor signaling pathway / Regulation of KIT signaling / Signaling by ALK / Platelet sensitization by LDL / positive regulation of natural killer cell mediated cytotoxicity / negative regulation of MAPK cascade / regulation of G1/S transition of mitotic cell cycle / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / negative regulation of interleukin-6 production / regulation of type I interferon-mediated signaling pathway / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of tumor necrosis factor production / peptidyl-tyrosine dephosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / PD-1 signaling / Regulation of IFNA/IFNB signaling / hematopoietic progenitor cell differentiation / Interleukin receptor SHC signaling / T cell proliferation / Regulation of IFNG signaling / Growth hormone receptor signaling / negative regulation of T cell proliferation / GPVI-mediated activation cascade / T cell costimulation / cell adhesion molecule binding / SH2 domain binding / phosphotyrosine residue binding / protein dephosphorylation / regulation of ERK1 and ERK2 cascade / protein-tyrosine-phosphatase / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein tyrosine phosphatase activity / B cell receptor signaling pathway / platelet aggregation / SH3 domain binding / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / specific granule lumen / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / MAPK cascade / cell-cell junction / Interferon alpha/beta signaling / transmembrane signaling receptor activity / tertiary granule lumen / mitotic cell cycle / T cell receptor signaling pathway / carbohydrate binding / regulation of apoptotic process / adaptive immune response / cell differentiation / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / intracellular signal transduction / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / external side of plasma membrane / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / nucleolus / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, restrained molecular dynamics | ||||||
Authors | Kasai, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the SHP-1 C-terminal SH2 domain complexed with a tyrosine-phosphorylated peptide from NKG2A Authors: Kasai, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yu7.cif.gz | 768.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yu7.ent.gz | 667.2 KB | Display | PDB format |
PDBx/mmJSON format | 2yu7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/2yu7 ftp://data.pdbj.org/pub/pdb/validation_reports/yu/2yu7 | 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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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12608.992 Da / Num. of mol.: 1 / Fragment: SH2 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: SHP1 / Plasmid: P040607-04 / References: UniProt: P29350, protein-tyrosine-phosphatase |
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#2: Protein/peptide | Mass: 1831.886 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The human NKG2A phosphorylated peptide is chemicaly synthesized. References: UniProt: P26715 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.89mM SHP1 SH2 domain U-15N,13C; 0.89mM NKG2A peptide; 20mM d-Tris-HCl (pH 7.4); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O | |||||||||||||||
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, restrained molecular dynamics Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |