[English] 日本語
![](img/lk-miru.gif)
- PDB-1d4w: CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP IN COMPLEX WITH SLAM PHO... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1d4w | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP IN COMPLEX WITH SLAM PHOSPHOPEPTIDE | ||||||
![]() |
| ||||||
![]() | SIGNALING PROTEIN / SH2 DOMAIN / PHOSPHOTYROSINE RECOGNIITON / PEPTIDE RECOGNITION / SIGNAL TRANSDUCTION / LYMPHOPROLIFERATIVE DISEASE | ||||||
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. / Terhorst, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 61.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 49.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 450.1 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 11702.393 Da / Num. of mol.: 2 / Fragment: SH2 DOMAIN / Mutation: RESIDUES 1-104 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1360.491 Da / Num. of mol.: 2 / Fragment: CYTOPLASMIC TAIL SYNTHETIC PHOSPOPEPTIDE / Source method: obtained synthetically / Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. / References: UniProt: Q13291 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.77 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 30% PEG 8000, 20% GLYCEROL, 100 MM SODIUM CITRATE, 10MM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 22K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 23946 / % possible obs: 94.8 % / Rmerge(I) obs: 0.076 |
Reflection | *PLUS Num. obs: 23946 / Num. measured all: 113987 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→10 Å / σ(F): 4 / Stereochemistry target values: ENGH& HUBER
| |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 4 / Rfactor Rfree: 0.24 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|