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Yorodumi- PDB-2rmx: Solution structure of the SHP-1 C-terminal SH2 domain complexed w... -
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-Basic information
Entry | Database: PDB / ID: 2rmx | ||||||
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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 / Alternative splicing / Cytoplasm / Hydrolase / Nucleus / Phosphoprotein / Protein phosphatase / Glycoprotein / Lectin / Membrane / Receptor / Signal-anchor / Transmembrane / 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 / negative regulation of T cell mediated cytotoxicity / epididymis development / negative regulation of inflammatory response to wounding / phosphorylation-dependent protein binding / transmembrane receptor protein tyrosine phosphatase activity / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / 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 / Signal regulatory protein family interactions / platelet formation / negative regulation of T cell receptor signaling pathway / megakaryocyte development / negative regulation of MAPK cascade / Regulation of KIT signaling / Signaling by ALK / Platelet sensitization by LDL / regulation of G1/S transition of mitotic cell cycle / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / regulation of type I interferon-mediated signaling pathway / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of IFNA/IFNB signaling / PD-1 signaling / Interleukin receptor SHC signaling / hematopoietic progenitor cell differentiation / Nuclear events stimulated by ALK signaling in cancer / Regulation of IFNG signaling / T cell proliferation / negative regulation of T cell proliferation / Growth hormone receptor signaling / cell adhesion molecule binding / GPVI-mediated activation cascade / T cell costimulation / phosphotyrosine residue binding / SH2 domain binding / protein dephosphorylation / protein-tyrosine-phosphatase / regulation of ERK1 and ERK2 cascade / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein tyrosine phosphatase activity / B cell receptor signaling pathway / cytokine-mediated signaling pathway / platelet aggregation / SH3 domain binding / peptidyl-tyrosine phosphorylation / specific granule lumen / transmembrane signaling receptor activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / MAPK cascade / Interferon alpha/beta signaling / cell-cell junction / tertiary granule lumen / mitotic cell cycle / T cell receptor signaling pathway / carbohydrate binding / regulation of apoptotic process / adaptive immune response / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / cell differentiation / 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 / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing | ||||||
Authors | Kasai, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Structural basis for the recognition of the two NKG2A immunoreceptor tyrosine-based inhibitory motifs (ITIMs) by the C-terminal SH2 domain of protein tyrosine phosphatase SHP-1 Authors: Koshiba, S. / Kasai, T. / Sato, M. / Tomizawa, T. / Motoda, Y. / Tochio, N. / Kobayashi, N. / Harada, T. / Inoue, M. / Tanaka, A. / 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 | 2rmx.cif.gz | 764.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rmx.ent.gz | 662.6 KB | Display | PDB format |
PDBx/mmJSON format | 2rmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rmx_validation.pdf.gz | 359.9 KB | Display | wwPDB validaton report |
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Full document | 2rmx_full_validation.pdf.gz | 612.4 KB | Display | |
Data in XML | 2rmx_validation.xml.gz | 60.1 KB | Display | |
Data in CIF | 2rmx_validation.cif.gz | 72.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/2rmx ftp://data.pdbj.org/pub/pdb/validation_reports/rm/2rmx | HTTPS FTP |
-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: 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: E. coli CELL-FREE / Gene: PTPN6, HCP, PTP1C / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: P29350, protein-tyrosine-phosphatase |
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#2: Protein/peptide | Mass: 1755.837 Da / Num. of mol.: 1 / Fragment: tyrosine phosphorylation site, UNP residues 1-15 / Source method: obtained synthetically Details: Peptide synthetic; This sequence occurs naturally in humans References: UniProt: P26715 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.8mM [U-13C; U-15N] SHP-1 C-terminal SH2 domain; 0.8mM tyrosine-phosphorylated peptide; 20mM [U-2H] TRIS; 100mM sodium chloride; 0.02% sodium azide; 1mM [U-2H] DTT; 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 120 / pH: 7.4 / Pressure: ambient / Temperature units: K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 2833 / NOE intraresidue total count: 531 / NOE long range total count: 1129 / NOE medium range total count: 416 / NOE sequential total count: 634 / Protein chi angle constraints total count: 300 / Protein other angle constraints total count: 168 / Protein phi angle constraints total count: 248 / Protein psi angle constraints total count: 248 | ||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 4.82 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 12.87 ° / Maximum upper distance constraint violation: 0.16 Å | ||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.0025 Å |