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- PDB-1x6c: Solution structures of the SH2 domain of human protein-tyrosine p... -

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Basic information

Entry
Database: PDB / ID: 1x6c
TitleSolution structures of the SH2 domain of human protein-tyrosine phosphatase SHP-1
ComponentsTyrosine-protein phosphatase, non-receptor type 6
KeywordsSIGNALING PROTEIN / SH2 domain / HCP / PTP1C / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / negative regulation of B cell receptor signaling pathway / regulation of B cell differentiation / epididymis development / CD27 signaling pathway / negative regulation of inflammatory response to wounding / transmembrane receptor protein tyrosine phosphatase activity / phosphorylation-dependent protein binding / Co-inhibition by BTLA ...negative regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of mast cell activation involved in immune response / negative regulation of B cell receptor signaling pathway / regulation of B cell differentiation / epididymis development / CD27 signaling pathway / negative regulation of inflammatory response to wounding / transmembrane receptor protein tyrosine phosphatase activity / phosphorylation-dependent protein binding / Co-inhibition by BTLA / negative regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of neutrophil activation / CD22 mediated BCR regulation / alpha-beta T cell receptor complex / regulation of release of sequestered calcium ion into cytosol / Interleukin-37 signaling / positive regulation of cell adhesion mediated by integrin / Signal regulatory protein family interactions / platelet formation / Regulation of KIT signaling / megakaryocyte development / Signaling by ALK / negative regulation of T cell receptor signaling pathway / natural killer cell mediated cytotoxicity / Platelet sensitization by LDL / regulation of type I interferon-mediated signaling pathway / PECAM1 interactions / regulation of G1/S transition of mitotic cell cycle / negative regulation of interleukin-6 production / Regulation of IFNA/IFNB signaling / peptidyl-tyrosine dephosphorylation / negative regulation of tumor necrosis factor production / Interleukin-3, Interleukin-5 and GM-CSF signaling / Co-inhibition by PD-1 / Interleukin receptor SHC signaling / negative regulation of MAPK cascade / Regulation of IFNG signaling / hematopoietic progenitor cell differentiation / Growth hormone receptor signaling / regulation of ERK1 and ERK2 cascade / T cell proliferation / Nuclear events stimulated by ALK signaling in cancer / protein dephosphorylation / GPVI-mediated activation cascade / cell adhesion molecule binding / negative regulation of T cell proliferation / T cell costimulation / phosphotyrosine residue binding / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / SH2 domain binding / negative regulation of innate immune response / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / T cell activation / negative regulation of angiogenesis / B cell receptor signaling pathway / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / SH3 domain binding / platelet aggregation / specific granule lumen / Interferon gamma signaling / Interferon alpha/beta signaling / MAPK cascade / tertiary granule lumen / cell-cell junction / mitotic cell cycle / T cell receptor signaling pathway / regulation of apoptotic process / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of cell population proliferation / Neutrophil degranulation / protein kinase binding / nucleolus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Protein-tyrosine phosphatase, non-receptor type-6, -11 / SH2 domain / SHC Adaptor Protein / 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 ...: / Protein-tyrosine phosphatase, non-receptor type-6, -11 / SH2 domain / SHC Adaptor Protein / 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
Tyrosine-protein phosphatase non-receptor type 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSato, M. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structures of the SH2 domain of human protein-tyrosine phosphatase SHP-1
Authors: Sato, M. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 17, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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_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_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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


Theoretical massNumber of molelcules
Total (without water)12,6091
Polymers12,6091
Non-polymers00
Water00
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, structures with the least restraint violations
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: Cell-free protein synthesis / Gene: PTPN6 / Plasmid: P040607-04 / References: UniProt: P29350, protein-tyrosine-phosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1mM SH2 domain U-15N, 13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 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
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9295Kobayashi, N.data analysis
CYANA1.0.7Guntert, P.structure solution
CYANA1.0.7Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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