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- PDB-1d4t: CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP IN COMPLEX WITH A SLAM P... -
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Basic information
Entry | Database: PDB / ID: 1d4t | ||||||
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Title | CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP IN COMPLEX WITH A SLAM PEPTIDE | ||||||
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![]() | SIGNALING PROTEIN / SH2 DOMAIN / TYROSINE KINASE / SIGNAL TRANSDUCTION / PEPTIDE RECOGNITION | ||||||
Function / homology | ![]() natural killer cell proliferation / regulation of vesicle fusion / negative regulation of CD40 signaling pathway / myeloid dendritic cell activation involved in immune response / negative regulation of T cell cytokine production / leukocyte chemotaxis involved in inflammatory response / positive regulation of dendritic cell chemotaxis / positive regulation of T-helper 1 cell cytokine production / natural killer cell differentiation / positive regulation of natural killer cell mediated cytotoxicity ...natural killer cell proliferation / regulation of vesicle fusion / negative regulation of CD40 signaling pathway / myeloid dendritic cell activation involved in immune response / negative regulation of T cell cytokine production / leukocyte chemotaxis involved in inflammatory response / positive regulation of dendritic cell chemotaxis / positive regulation of T-helper 1 cell cytokine production / natural killer cell differentiation / positive regulation of natural killer cell mediated cytotoxicity / negative regulation of interleukin-12 production / natural killer cell mediated cytotoxicity / negative regulation of T cell receptor signaling pathway / positive regulation of macrophage chemotaxis / positive regulation of activated T cell proliferation / negative regulation of interleukin-6 production / humoral immune response / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / regulation of immune response / cellular defense response / phagocytosis / phagocytic vesicle / SH2 domain binding / positive regulation of JNK cascade / antigen binding / transmembrane signaling receptor activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / cell-cell signaling / virus receptor activity / signaling receptor activity / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / cell adhesion / external side of plasma membrane / innate immune response / positive regulation of cell population proliferation / extracellular exosome / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Poy, F. / Yaffe, M.B. / Sayos, J. / Saxena, K. / Eck, M.J. | ||||||
![]() | ![]() Title: Crystal structures of the XLP protein SAP reveal a class of SH2 domains with extended, phosphotyrosine-independent sequence recognition. Authors: Poy, F. / Yaffe, M.B. / Sayos, J. / Saxena, K. / Morra, M. / Sumegi, J. / Cantley, L.C. / Terhorst, C. / Eck, M.J. #1: ![]() Title: The X-linked lymphoproliferative disease gene product SAP regulates signals induced through the co-receptor SLAM Authors: Sayos, J. / Wu, C. / Morra, M. / Wang, N. / Terhosrt, C. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.7 KB | Display | ![]() |
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PDB format | ![]() | 49.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.5 KB | Display | ![]() |
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Full document | ![]() | 418.9 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11702.393 Da / Num. of mol.: 1 / Fragment: SH2 DOMAIN (RESIDUES 1-104) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1280.512 Da / Num. of mol.: 1 / Fragment: SLAM TAIL PEPTIDE (RESIDUES 276 TO 286) / Source method: obtained synthetically Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE NATURALLY OCCURS IN HUMANS (HOMO SAPIENS) References: UniProt: Q13291 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1 Å3/Da / Density % sol: 35.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 30% PEG 8000, 20% GLYCEROL, 100 MM HEPES PH 8.0, AND 100 MM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 22K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PRINCETON 2K / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→22 Å / Num. all: 34081 / % possible obs: 86 % / Rmerge(I) obs: 0.043 |
Reflection | *PLUS Highest resolution: 1.1 Å / Num. obs: 34081 / % possible obs: 86 % / Num. measured all: 134878 |
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Processing
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.1→8 Å / Num. parameters: 1032 / Num. restraintsaints: 1219 / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Occupancy sum hydrogen: 957 / Occupancy sum non hydrogen: 1147 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 4 / Num. reflection Rfree: 171 / % reflection Rfree: 5 % / Rfactor Rwork: 0.13 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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