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- PDB-2yu7: Solution structure of the SHP-1 C-terminal SH2 domain complexed w... -

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Basic information

Entry
Database: PDB / ID: 2yu7
TitleSolution structure of the SHP-1 C-terminal SH2 domain complexed with a tyrosine-phosphorylated peptide from NKG2A
Components
  • Tyrosine-protein phosphatase non-receptor type 6
  • natural killer group 2A
KeywordsSIGNALING PROTEIN / SH2 domain / Protein-peptide complex / Phosphorylated peptide recognition / Phosphotyrosine binding domain / Signal Transduction / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


inhibitory MHC class Ib receptor activity / CD8-positive, gamma-delta intraepithelial T cell differentiation / HLA-E specific inhibitory MHC class Ib receptor activity / natural killer cell inhibitory signaling pathway / negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / MHC class I protein complex binding / regulation of B cell differentiation / regulation of natural killer cell activation / negative regulation of peptidyl-tyrosine phosphorylation ...inhibitory MHC class Ib receptor activity / CD8-positive, gamma-delta intraepithelial T cell differentiation / HLA-E specific inhibitory MHC class Ib receptor activity / natural killer cell inhibitory signaling pathway / negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / MHC class I protein complex binding / regulation of B cell differentiation / regulation of natural killer cell activation / negative regulation of peptidyl-tyrosine phosphorylation / epididymis development / negative regulation of T cell mediated cytotoxicity / phosphorylation-dependent protein binding / negative regulation of inflammatory response to wounding / transmembrane receptor protein tyrosine phosphatase activity / natural killer cell mediated cytotoxicity / alpha-beta T cell receptor complex / regulation of release of sequestered calcium ion into cytosol / CD22 mediated BCR regulation / Interleukin-37 signaling / positive regulation of cell adhesion mediated by integrin / Costimulation by the CD28 family / negative regulation of natural killer cell mediated cytotoxicity / Signal regulatory protein family interactions / platelet formation / megakaryocyte development / negative regulation of T cell receptor signaling pathway / Regulation of KIT signaling / Signaling by ALK / Platelet sensitization by LDL / positive regulation of natural killer cell mediated cytotoxicity / negative regulation of MAPK cascade / regulation of G1/S transition of mitotic cell cycle / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / negative regulation of interleukin-6 production / regulation of type I interferon-mediated signaling pathway / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of tumor necrosis factor production / peptidyl-tyrosine dephosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of IFNA/IFNB signaling / PD-1 signaling / Interleukin receptor SHC signaling / hematopoietic progenitor cell differentiation / T cell proliferation / Regulation of IFNG signaling / Growth hormone receptor signaling / negative regulation of T cell proliferation / GPVI-mediated activation cascade / T cell costimulation / cell adhesion molecule binding / phosphotyrosine residue binding / SH2 domain binding / protein dephosphorylation / regulation of ERK1 and ERK2 cascade / protein-tyrosine-phosphatase / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein tyrosine phosphatase activity / B cell receptor signaling pathway / platelet aggregation / SH3 domain binding / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / specific granule lumen / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / MAPK cascade / Interferon alpha/beta signaling / cell-cell junction / transmembrane signaling receptor activity / tertiary granule lumen / mitotic cell cycle / T cell receptor signaling pathway / carbohydrate binding / regulation of apoptotic process / adaptive immune response / cell differentiation / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / intracellular signal transduction / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / external side of plasma membrane / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / nucleolus / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Natural killer cell receptor-like, C-type lectin-like domain / Protein-tyrosine phosphatase, non-receptor type-6, -11 / SH2 domain / SHC Adaptor Protein / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold ...Natural killer cell receptor-like, C-type lectin-like domain / Protein-tyrosine phosphatase, non-receptor type-6, -11 / SH2 domain / SHC Adaptor Protein / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NKG2-A/NKG2-B type II integral membrane protein / Tyrosine-protein phosphatase non-receptor type 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsKasai, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the SHP-1 C-terminal SH2 domain complexed with a tyrosine-phosphorylated peptide from NKG2A
Authors: Kasai, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionApr 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 6
B: natural killer group 2A


Theoretical massNumber of molelcules
Total (without water)14,4412
Polymers14,4412
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 6 / SH2-domain phosphatase 1 / Protein-tyrosine phosphatase 1C / PTP-1C / Hematopoietic cell protein- ...SH2-domain phosphatase 1 / Protein-tyrosine phosphatase 1C / PTP-1C / Hematopoietic cell protein-tyrosine phosphatase / SH-PTP1 / Protein-tyrosine phosphatase SHP-1


Mass: 12608.992 Da / Num. of mol.: 1 / Fragment: SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: SHP1 / Plasmid: P040607-04 / References: UniProt: P29350, protein-tyrosine-phosphatase
#2: Protein/peptide natural killer group 2A / NKG2A


Mass: 1831.886 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The human NKG2A phosphorylated peptide is chemicaly synthesized.
References: UniProt: P26715

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
2313D F1-15N,13C-filtered 15N-separated NOESY
1413D F1-15N,13C-filtered 13C-separated NOESY
2512D F2-15N,13C-filtered NOESY

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Sample preparation

DetailsContents: 0.89mM SHP1 SH2 domain U-15N,13C; 0.89mM NKG2A peptide; 20mM d-Tris-HCl (pH 7.4); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1120mM 7.4 ambient 296 K
2120mM 7.4 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.981Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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