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- PDB-1wa7: SH3 DOMAIN OF HUMAN LYN TYROSINE KINASE IN COMPLEX WITH A HERPESV... -

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Basic information

Entry
Database: PDB / ID: 1wa7
TitleSH3 DOMAIN OF HUMAN LYN TYROSINE KINASE IN COMPLEX WITH A HERPESVIRAL LIGAND
Components
  • HYPOTHETICAL 28.7 KDA PROTEIN IN DHFR 3'REGION (ORF1)
  • TYROSINE-PROTEIN KINASE LYN
KeywordsSH3 DOMAIN / LIGAND / TYROSINE KINASE / SIGNAL TRANSDUCTION / LYN / TIP / PROTO-ONCOGENE / HYPOTHETICAL PROTEIN
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 / Fc receptor mediated stimulatory signaling pathway / positive regulation of Fc receptor mediated stimulatory signaling pathway / positive regulation of dendritic cell apoptotic process ...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 / Fc receptor mediated stimulatory signaling pathway / positive regulation of Fc receptor mediated stimulatory signaling pathway / positive regulation of dendritic cell apoptotic process / positive regulation of oligodendrocyte progenitor proliferation / 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 / phosphorylation-dependent protein binding / negative regulation of toll-like receptor 4 signaling pathway / regulation of mast cell degranulation / platelet degranulation / dendritic cell differentiation / regulation of platelet aggregation / : / regulation of B cell apoptotic process / oligodendrocyte development / phosphatidylinositol 3-kinase activator activity / Signaling by Erythropoietin / histamine secretion by mast cell / Erythropoietin activates STAT5 / interleukin-5-mediated signaling pathway / Erythropoietin activates Phospholipase C gamma (PLCG) / Platelet Adhesion to exposed collagen / CD28 co-stimulation / negative regulation of immune response / regulation of release of sequestered calcium ion into cytosol / CD22 mediated BCR regulation / gamma-tubulin binding / platelet-derived growth factor receptor binding / response to carbohydrate / Fc epsilon receptor (FCERI) signaling / EPH-Ephrin signaling / toll-like receptor 4 signaling pathway / Regulation of KIT signaling / postsynaptic specialization, intracellular component / CTLA4 inhibitory signaling / leukocyte migration / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Fc-gamma receptor signaling pathway involved in phagocytosis / EPHA-mediated growth cone collapse / Dectin-2 family / negative regulation of B cell proliferation / mitochondrial crista / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / Fc-epsilon receptor signaling pathway / regulation of cell adhesion mediated by integrin / B cell homeostasis / FCGR activation / EPH-ephrin mediated repulsion of cells / response to axon injury / ephrin receptor signaling pathway / response to amino acid / Role of LAT2/NTAL/LAB on calcium mobilization / growth hormone receptor signaling pathway via JAK-STAT / hematopoietic progenitor cell differentiation / Erythropoietin activates RAS / cellular response to retinoic acid / Growth hormone receptor signaling / Signaling by CSF3 (G-CSF) / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of glial cell proliferation / lipopolysaccharide-mediated signaling pathway / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of inflammatory response to antigenic stimulus / GPVI-mediated activation cascade / cell surface receptor protein tyrosine kinase signaling pathway / regulation of cytokine production / T cell costimulation / EPHB-mediated forward signaling / viral process / ephrin receptor binding / CD209 (DC-SIGN) signaling / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / erythrocyte differentiation / regulation of ERK1 and ERK2 cascade / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / negative regulation of protein phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / response to hormone / negative regulation of MAP kinase activity / DNA damage checkpoint signaling / Regulation of signaling by CBL / Cell surface interactions at the vascular wall / phosphoprotein binding
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 / SH3 type barrels. / SH2 domain / Src homology 3 domains ...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 / SH3 type barrels. / SH2 domain / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 / Tyrosine-protein kinase-interacting protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SAIMIRIINE HERPESVIRUS 2 (Herpesvirus saimiri)
MethodSOLUTION NMR / XPLOR
AuthorsBauer, F. / Schweimer, K. / Hoffmann, S. / Roesch, P. / Sticht, H.
CitationJournal: Biochemistry / Year: 2002
Title: Structural Investigation of the Binding of a Herpesviral Protein to the SH3 Domain of Tyrosine Kinase Lck.
Authors: Schweimer, K. / Hoffmann, S. / Bauer, F. / Friedrich, U. / Kardinal, C. / Feller, S.M. / Biesinger, B. / Sticht, H.
History
DepositionOct 25, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYROSINE-PROTEIN KINASE LYN
B: HYPOTHETICAL 28.7 KDA PROTEIN IN DHFR 3'REGION (ORF1)


Theoretical massNumber of molelcules
Total (without water)9,7742
Polymers9,7742
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 39-101
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: INTRACELLULAR / Plasmid: PGEX-6P-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P07948, EC: 2.7.1.112
#2: Protein/peptide HYPOTHETICAL 28.7 KDA PROTEIN IN DHFR 3'REGION (ORF1) / TIP


Mass: 2399.724 Da / Num. of mol.: 1
Fragment: TYROSINE KINASE INTERACTION PROTEIN, RESIDUES 170-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SAIMIRIINE HERPESVIRUS 2 (Herpesvirus saimiri)
Strain: 488 / Variant: SUBGROUP C / Plasmid: PGEX-4T-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P22575

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-EDITED NOESY
1213D 15N- EDITED NOESY
2323D 13C- EDITED NOESY
2423D 15N-EDITED NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED LYNSH3 AND TIP

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Sample preparation

Details
Solution-IDContents
190% WATER/10% D2O, 2.5 MMOL/L
290% WATER/10% D2O, 1.5 MMOL/L
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1150 mM6.4 1.0 atm298.0 K
2150 mM6.4 1.0 atm298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE8002

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Processing

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

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