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- PDB-1w1f: SH3 DOMAIN OF HUMAN LYN TYROSINE KINASE -

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Basic information

Entry
Database: PDB / ID: 1w1f
TitleSH3 DOMAIN OF HUMAN LYN TYROSINE KINASE
ComponentsTYROSINE-PROTEIN KINASE LYN
KeywordsSH3-DOMAIN / SH3 DOMAIN / TYROSINE KINASE / SIGNAL TRANSDUCTION / LYN
Function / homology
Function and homology information


C-X-C chemokine receptor CXCR4 signaling pathway / regulation of monocyte chemotaxis / negative regulation of intracellular signal transduction / response to sterol depletion / regulation of mast cell activation / negative regulation of myeloid leukocyte differentiation / eosinophil differentiation / positive regulation of dendritic cell apoptotic process / Fc receptor mediated stimulatory signaling pathway / positive regulation of oligodendrocyte progenitor proliferation ...C-X-C chemokine receptor CXCR4 signaling pathway / regulation of monocyte chemotaxis / negative regulation of intracellular signal transduction / response to sterol depletion / regulation of mast cell activation / negative regulation of myeloid leukocyte differentiation / eosinophil differentiation / positive regulation of dendritic cell apoptotic process / Fc receptor mediated stimulatory signaling pathway / positive regulation of oligodendrocyte progenitor proliferation / positive regulation of Fc receptor mediated stimulatory signaling pathway / Fc receptor mediated inhibitory signaling pathway / regulation of B cell receptor signaling pathway / tolerance induction to self antigen / negative regulation of toll-like receptor 2 signaling pathway / integrin alpha2-beta1 complex / immune response-regulating cell surface receptor signaling pathway / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / positive regulation of mast cell proliferation / negative regulation of mast cell proliferation / glycosphingolipid binding / platelet degranulation / negative regulation of toll-like receptor 4 signaling pathway / regulation of mast cell degranulation / phosphorylation-dependent protein binding / regulation of platelet aggregation / dendritic cell differentiation / regulation of B cell apoptotic process / phosphatidylinositol 3-kinase activator activity / oligodendrocyte development / Signaling by Erythropoietin / response to carbohydrate / Erythropoietin activates STAT5 / interleukin-5-mediated signaling pathway / Erythropoietin activates Phospholipase C gamma (PLCG) / CD28 co-stimulation / Platelet Adhesion to exposed collagen / negative regulation of immune response / histamine secretion by mast cell / regulation of release of sequestered calcium ion into cytosol / CD22 mediated BCR regulation / platelet-derived growth factor receptor binding / gamma-tubulin binding / EPH-Ephrin signaling / Fc epsilon receptor (FCERI) signaling / toll-like receptor 4 signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / Regulation of KIT signaling / postsynaptic specialization, intracellular component / leukocyte migration / CTLA4 inhibitory signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / EPHA-mediated growth cone collapse / Dectin-2 family / negative regulation of B cell proliferation / B cell homeostasis / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / mitochondrial crista / PECAM1 interactions / regulation of cell adhesion mediated by integrin / FCGR activation / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / response to axon injury / response to amino acid / growth hormone receptor signaling pathway via JAK-STAT / Role of LAT2/NTAL/LAB on calcium mobilization / hematopoietic progenitor cell differentiation / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / fatty acid transport / Growth hormone receptor signaling / cell surface receptor protein tyrosine kinase signaling pathway / lipopolysaccharide-mediated signaling pathway / cellular response to retinoic acid / positive regulation of tyrosine phosphorylation of STAT protein / negative regulation of MAP kinase activity / positive regulation of glial cell proliferation / GPVI-mediated activation cascade / T cell costimulation / regulation of cytokine production / EPHB-mediated forward signaling / ephrin receptor binding / CD209 (DC-SIGN) signaling / regulation of ERK1 and ERK2 cascade / response to hormone / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / negative regulation of protein phosphorylation / erythrocyte differentiation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / DNA damage checkpoint signaling / Regulation of signaling by CBL / negative regulation of inflammatory response to antigenic stimulus / Cell surface interactions at the vascular wall / non-specific protein-tyrosine kinase / FCGR3A-mediated phagocytosis / adherens junction
Similarity search - Function
Tyrosine-protein kinase Lyn, SH3 domain / Tyrosine-protein kinase Lyn, SH2 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. ...Tyrosine-protein kinase Lyn, SH3 domain / Tyrosine-protein kinase Lyn, SH2 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / 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 kinase Lyn
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / X-PLOR
AuthorsBauer, F. / Schweimer, K. / Hoffmann, S. / Roesch, P. / Sticht, H.
CitationJournal: Protein Sci. / Year: 2005
Title: Structural Characterization of Lyn-SH3 Domain in Complex with a Herpesviral Protein Reveals an Extended Recognition Motif that Enhances Binding Affinity.
Authors: Bauer, F. / Schweimer, K. / Meiselbach, H. / Hoffmann, S. / Roesch, P. / Sticht, H.
History
DepositionJun 17, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYROSINE-PROTEIN KINASE LYN


Theoretical massNumber of molelcules
Total (without water)7,3741
Polymers7,3741
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 / 60LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein TYROSINE-PROTEIN KINASE LYN


Mass: 7374.357 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN, RESIDUES 60-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P07948, EC: 2.7.1.112

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 13C-
12115N-EDITED NOESY
1313D 15N-EDITED NOESY
1413D 13C-EDITED NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED LYNSH3

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Sample preparation

Sample conditionsIonic strength: 150 mM / pH: 6.4 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker OTHER / Manufacturer: Bruker / Model: OTHER / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
NMRViewstructure solution
RefinementMethod: X-PLOR / Software ordinal: 1 / Details: AB INITIO SIMULATED ANNEALING
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 60 / Conformers submitted total number: 20

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