+Open data
-Basic information
Entry | Database: PDB / ID: 1ka7 | ||||||
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Title | SAP/SH2D1A bound to peptide n-Y-c | ||||||
Components |
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Keywords | IMMUNE SYSTEM / SH2 domain / protein-peptide complex | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model type details | minimized average | ||||||
Authors | Hwang, P.M. / Li, C. / Morra, M. / Lillywhite, J. / Gertler, F. / Terhorst, C. / Kay, L.E. / Pawson, T. / Forman-Kay, J. / Li, S.-C. | ||||||
Citation | Journal: EMBO J. / Year: 2002 Title: A "three-pronged" binding mechanism for the SAP/SH2D1A SH2 domain: structural basis and relevance to the XLP syndrome. Authors: Hwang, P.M. / Li, C. / Morra, M. / Lillywhite, J. / Muhandiram, D.R. / Gertler, F. / Terhorst, C. / Kay, L.E. / Pawson, T. / Forman-Kay, J.D. / Li, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ka7.cif.gz | 52.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ka7.ent.gz | 38 KB | Display | PDB format |
PDBx/mmJSON format | 1ka7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ka7_validation.pdf.gz | 249.6 KB | Display | wwPDB validaton report |
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Full document | 1ka7_full_validation.pdf.gz | 249.3 KB | Display | |
Data in XML | 1ka7_validation.xml.gz | 3.7 KB | Display | |
Data in CIF | 1ka7_validation.cif.gz | 4.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/1ka7 ftp://data.pdbj.org/pub/pdb/validation_reports/ka/1ka7 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 14206.181 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O60880 |
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#2: Protein/peptide | Mass: 1437.706 Da / Num. of mol.: 1 / Fragment: Cytoplasmic region (residues 275-286) / Mutation: K275R / Source method: obtained synthetically Details: This peptide was chemically synthesized (solid phase synthesis). The sequence of the peptide is naturally found in Homo sapiens (human). References: UniProt: Q13291 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details | Contents: 1 mM SAP U-15N, 13C; 1mM n-pY; 20 mM phosphate buffer, 100mM NaCl Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120 mM / pH: 6.0 / Pressure: ambient / Temperature: 303 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||
NMR ensemble | Conformers submitted total number: 1 |