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

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Basic information

Entry
Database: PDB / ID: 2rmx
TitleSolution structure of the SHP-1 C-terminal SH2 domain complexed with a tyrosine-phosphorylated peptide from NKG2A
Components
  • NKG2-A/NKG2-B type II integral membrane protein
  • Tyrosine-protein phosphatase non-receptor type 6
KeywordsSIGNALING PROTEIN / SH2 domain / protein-peptide complex / phosphorylated peptide recognition / phosphotyrosine binding domain / signal transduction / Alternative splicing / Cytoplasm / Hydrolase / Nucleus / Phosphoprotein / Protein phosphatase / Glycoprotein / Lectin / Membrane / Receptor / Signal-anchor / Transmembrane / 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 / PD-1 signaling / Regulation of IFNA/IFNB 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 / SH2 domain binding / phosphotyrosine residue 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 / cell-cell junction / Interferon alpha/beta signaling / 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, simulated annealing
AuthorsKasai, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structural basis for the recognition of the two NKG2A immunoreceptor tyrosine-based inhibitory motifs (ITIMs) by the C-terminal SH2 domain of protein tyrosine phosphatase SHP-1
Authors: Koshiba, S. / Kasai, T. / Sato, M. / Tomizawa, T. / Motoda, Y. / Tochio, N. / Kobayashi, N. / Harada, T. / Inoue, M. / Tanaka, A. / Kigawa, T. / Yokoyama, S.
History
DepositionNov 30, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 2, 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

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 6
B: NKG2-A/NKG2-B type II integral membrane protein


Theoretical massNumber of molelcules
Total (without water)14,3652
Polymers14,3652
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 6 / Protein-tyrosine phosphatase 1C / PTP-1C / Hematopoietic cell protein-tyrosine phosphatase / SH- ...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: E. coli CELL-FREE / Gene: PTPN6, HCP, PTP1C / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: P29350, protein-tyrosine-phosphatase
#2: Protein/peptide NKG2-A/NKG2-B type II integral membrane protein / NKG2-A/B-activating NK receptor / NK cell receptor A / CD159a antigen


Mass: 1755.837 Da / Num. of mol.: 1 / Fragment: tyrosine phosphorylation site, UNP residues 1-15 / Source method: obtained synthetically
Details: Peptide synthetic; This sequence occurs naturally in humans
References: UniProt: P26715

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D F1-15N,13C-filtered 15N-separated NOESY
1413D F1-15N,13C-filtered 13C-separated NOESY
1512D F2-15N,13C-filtered NOESY

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Sample preparation

DetailsContents: 0.8mM [U-13C; U-15N] SHP-1 C-terminal SH2 domain; 0.8mM tyrosine-phosphorylated peptide; 20mM [U-2H] TRIS; 100mM sodium chloride; 0.02% sodium azide; 1mM [U-2H] DTT; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMentity_1[U-13C; U-15N]1
0.8 mMentity_21
20 mMTRIS[U-2H]1
100 mMsodium chloride1
0.02 %sodium azide1
1 mMDTT[U-2H]1
Sample conditionsIonic strength: 120 / pH: 7.4 / Pressure: ambient / Temperature units: K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.6Bruker Biospincollection
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.0.4Johnson, One Moon Scientificdata analysis
NMRView5.0.4Johnson, One Moon Scientificpeak picking
NMRView5.0.4Johnson, One Moon Scientificchemical shift assignment
KUJIRA0.981Kobayashi, N.data analysis
KUJIRA0.981Kobayashi, N.peak picking
KUJIRA0.981Kobayashi, N.chemical shift assignment
CYANA2.0.17Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.0.17Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2833 / NOE intraresidue total count: 531 / NOE long range total count: 1129 / NOE medium range total count: 416 / NOE sequential total count: 634 / Protein chi angle constraints total count: 300 / Protein other angle constraints total count: 168 / Protein phi angle constraints total count: 248 / Protein psi angle constraints total count: 248
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 4.82 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 12.87 ° / Maximum upper distance constraint violation: 0.16 Å
NMR ensemble rmsDistance rms dev: 0.0025 Å

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