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Open data
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Basic information
Entry | Database: PDB / ID: 1i3z | ||||||
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Title | MURINE EAT2 SH2 DOMAIN IN COMPLEX WITH SLAM PHOSPHOPEPTIDE | ||||||
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![]() | SIGNALING PROTEIN / SH2 domain Phosphotyrosine signal transduction lymphocyte | ||||||
Function / homology | ![]() natural killer cell inhibitory signaling pathway / 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 natural killer cell mediated immunity / positive regulation of dendritic cell chemotaxis / negative regulation of peptidyl-tyrosine phosphorylation ...natural killer cell inhibitory signaling pathway / 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 natural killer cell mediated immunity / positive regulation of dendritic cell chemotaxis / negative regulation of peptidyl-tyrosine phosphorylation / positive regulation of signal transduction / positive regulation of T-helper 1 cell cytokine production / natural killer cell differentiation / negative regulation of natural killer cell mediated cytotoxicity / leukocyte activation involved in immune response / positive regulation of natural killer cell mediated cytotoxicity / negative regulation of interleukin-12 production / positive regulation of innate immune response / positive regulation of macrophage chemotaxis / positive regulation of activated T cell proliferation / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / phagocytosis / signaling adaptor activity / phagocytic vesicle / phosphotyrosine residue binding / SH2 domain binding / positive regulation of JNK cascade / antigen binding / peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of type II interferon production / 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 Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lu, J. / Poy, F. / Morra, M. / Terhorst, C. / Eck, M.J. | ||||||
![]() | ![]() Title: Structural basis for the interaction of the free SH2 domain EAT-2 with SLAM receptors in hematopoietic cells. Authors: Morra, M. / Lu, J. / Poy, F. / Martin, M. / Sayos, J. / Calpe, S. / Gullo, C. / Howie, D. / Rietdijk, S. / Thompson, A. / Coyle, A.J. / Denny, C. / Yaffe, M.B. / Engel, P. / Eck, M.J. / Terhorst, C. #1: ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.5 KB | Display | ![]() |
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PDB format | ![]() | 25.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.8 KB | Display | ![]() |
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Full document | ![]() | 443.1 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar 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: 11781.718 Da / Num. of mol.: 1 / Fragment: SH2 DOMAIN (RESIDUES 1-103) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1717.915 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This peptide was chemically synthesized. The sequence of this peptide is naturally found in Homo sapiens (humans). References: GenBank: 9588411, UniProt: Q13291*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.82 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M sodium citrate, 30% PEG 8000, 10mM DTT, 25 mM ammonium sulphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 5.6 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2000 / Details: osmic |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 7460 / Num. obs: 7460 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.1→2.16 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2 / % possible all: 75 |
Reflection | *PLUS % possible obs: 97 % / Num. measured all: 24668 |
Reflection shell | *PLUS Rmerge(I) obs: 0.33 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: SAP SH2 Resolution: 2.15→5 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 34.396 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→5 Å
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor all: 0.231 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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