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- PDB-1jeg: Solution structure of the SH3 domain from C-terminal Src Kinase c... -

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Basic information

Entry
Database: PDB / ID: 1jeg
TitleSolution structure of the SH3 domain from C-terminal Src Kinase complexed with a peptide from the tyrosine phosphatase PEP
Components
  • HEMATOPOIETIC CELL PROTEIN-TYROSINE PHOSPHATASE 70Z-PEP
  • TYROSINE-PROTEIN KINASE CSK
KeywordsTRANSFERASE/HYDROLASE / SH3 domain / protein-peptide complex / tyrosine phosphatase / kinase / TRANSFERASE-HYDROLASE COMPLEX
Function / homology
Function and homology information


positive regulation of granzyme B production / phosphoanandamide dephosphorylation / histone H2AXY142 kinase activity / negative regulation of Golgi to plasma membrane protein transport / RHOH GTPase cycle / GAB1 signalosome / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Negative regulation of FLT3 / regulation of Fc receptor mediated stimulatory signaling pathway ...positive regulation of granzyme B production / phosphoanandamide dephosphorylation / histone H2AXY142 kinase activity / negative regulation of Golgi to plasma membrane protein transport / RHOH GTPase cycle / GAB1 signalosome / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Negative regulation of FLT3 / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of toll-like receptor 3 signaling pathway / regulation of natural killer cell proliferation / Co-inhibition by PD-1 / regulation of leukocyte migration / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of toll-like receptor 9 signaling pathway / Integrin signaling / MAP2K and MAPK activation / regulation of non-canonical NF-kappaB signal transduction / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of p38MAPK cascade / negative regulation of low-density lipoprotein particle clearance / positive regulation of protein K63-linked ubiquitination / cellular response to muramyl dipeptide / negative regulation of T cell activation / histone H3Y41 kinase activity / negative regulation of interleukin-8 production / regulation of calcium ion transmembrane transport / adherens junction organization / proline-rich region binding / negative regulation of bone resorption / regulation of T cell activation / cellular response to peptide hormone stimulus / negative regulation of phagocytosis / positive regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of T cell receptor signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / protein kinase A catalytic subunit binding / oligodendrocyte differentiation / negative regulation of interleukin-6 production / positive regulation of interferon-alpha production / negative regulation of tumor necrosis factor production / T cell differentiation / protein dephosphorylation / positive regulation of defense response to virus by host / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / positive regulation of interferon-beta production / protein tyrosine kinase binding / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / negative regulation of ERK1 and ERK2 cascade / SH3 domain binding / lipid metabolic process / autophagy / cytoplasmic side of plasma membrane / kinase binding / positive regulation of protein import into nucleus / cell-cell junction / T cell receptor signaling pathway / transferase activity / protein tyrosine kinase activity / protein phosphatase binding / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / intracellular signal transduction / protein phosphorylation / negative regulation of cell population proliferation / negative regulation of gene expression / positive regulation of gene expression / perinuclear region of cytoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Non-receptor tyrosine-protein phosphatase 22 / : / CSK-like, SH2 domain / : / SH3 Domains / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / : ...Non-receptor tyrosine-protein phosphatase 22 / : / CSK-like, SH2 domain / : / SH3 Domains / 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 / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 22 / Tyrosine-protein kinase CSK
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, torsional angle dynmaics
AuthorsGhose, R. / Shekhtman, A. / Goger, M.J. / Ji, H. / Cowburn, D.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: A novel, specific interaction involving the Csk SH3 domain and its natural ligand.
Authors: Ghose, R. / Shekhtman, A. / Goger, M.J. / Ji, H. / Cowburn, D.
History
DepositionJun 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYROSINE-PROTEIN KINASE CSK
B: HEMATOPOIETIC CELL PROTEIN-TYROSINE PHOSPHATASE 70Z-PEP


Theoretical massNumber of molelcules
Total (without water)12,1112
Polymers12,1112
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)25 / 1000structures with the lowest energy
Representative

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Components

#1: Protein TYROSINE-PROTEIN KINASE CSK / C-SRC KINASE / PROTEIN-TYROSINE KINASE CYL


Mass: 9198.627 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P41241, EC: 2.7.1.112
#2: Protein/peptide HEMATOPOIETIC CELL PROTEIN-TYROSINE PHOSPHATASE 70Z-PEP


Mass: 2912.187 Da / Num. of mol.: 1 / Fragment: 25 residue peptide (residues 612-629)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P29352, protein-tyrosine-phosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 7.2 / Pressure: 1 atm / Temperature: 293 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentert, Mumenthaler, Hermannstructure solution
DYANA1.5Guentert, Mumenthaler, Hermannrefinement
RefinementMethod: simulated annealing, torsional angle dynmaics / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 25

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