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- PDB-1ka7: SAP/SH2D1A bound to peptide n-Y-c -

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Basic information

Entry
Database: PDB / ID: 1ka7
TitleSAP/SH2D1A bound to peptide n-Y-c
Components
  • SH2 DOMAIN PROTEIN 1A
  • peptide n-Y-c
KeywordsIMMUNE 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 / leukocyte chemotaxis involved in inflammatory response / negative regulation of T cell cytokine production / positive regulation of dendritic cell chemotaxis / positive regulation of T-helper 1 cell cytokine production / natural killer cell differentiation / negative regulation of interleukin-12 production ...natural killer cell proliferation / regulation of vesicle fusion / negative regulation of CD40 signaling pathway / myeloid dendritic cell activation involved in immune response / leukocyte chemotaxis involved in inflammatory response / negative regulation of T cell cytokine production / positive regulation of dendritic cell chemotaxis / positive regulation of T-helper 1 cell cytokine production / natural killer cell differentiation / 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 natural killer cell mediated cytotoxicity / 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 / phagocytic vesicle / phagocytosis / antigen binding / SH2 domain binding / positive regulation of JNK cascade / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / positive regulation of type II interferon production / virus receptor activity / cell-cell signaling / 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 / cytosol / cytoplasm
Similarity search - Function
SH2 protein 1A / SH2D1A, SH2 domain / Signaling lymphocytic activation molecule, N-terminal / Signaling lymphocytic activation molecule (SLAM) protein / SH2 domain / SHC Adaptor Protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain ...SH2 protein 1A / SH2D1A, SH2 domain / Signaling lymphocytic activation molecule, N-terminal / Signaling lymphocytic activation molecule (SLAM) protein / SH2 domain / SHC Adaptor Protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SH2 domain-containing protein 1A / Signaling lymphocytic activation molecule
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsHwang, P.M. / Li, C. / Morra, M. / Lillywhite, J. / Gertler, F. / Terhorst, C. / Kay, L.E. / Pawson, T. / Forman-Kay, J. / Li, S.-C.
CitationJournal: 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
DepositionOct 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SH2 DOMAIN PROTEIN 1A
B: peptide n-Y-c


Theoretical massNumber of molelcules
Total (without water)15,6442
Polymers15,6442
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein SH2 DOMAIN PROTEIN 1A / / SLAM-ASSOCIATED 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
#2: Protein/peptide peptide n-Y-c / SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N,13C-separated NOESY
1213D HNHB
1313D HN(CO)HB
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1 mM SAP U-15N, 13C; 1mM n-pY; 20 mM phosphate buffer, 100mM NaCl
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120 mM / pH: 6.0 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1Nilgesstructure solution
NMRPipe1.8Delaglioprocessing
NMRView3Johnsondata analysis
ARIA1Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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