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- PDB-1gl5: NMR structure of the SH3 domain from the Tec protein tyrosine kinase -

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Basic information

Entry
Database: PDB / ID: 1gl5
TitleNMR structure of the SH3 domain from the Tec protein tyrosine kinase
ComponentsTYROSINE-PROTEIN KINASE TEC
KeywordsTRANSFERASE / TYROSINE-PROTEIN KINASE / ATP-BINDING / SH3 DOMAIN / PHOSPHORYLATION
Function / homology
Function and homology information


Signaling by SCF-KIT / FCERI mediated Ca+2 mobilization / regulation of platelet activation / tissue regeneration / Interleukin-3, Interleukin-5 and GM-CSF signaling / peptidyl-tyrosine autophosphorylation / integrin-mediated signaling pathway / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity ...Signaling by SCF-KIT / FCERI mediated Ca+2 mobilization / regulation of platelet activation / tissue regeneration / Interleukin-3, Interleukin-5 and GM-CSF signaling / peptidyl-tyrosine autophosphorylation / integrin-mediated signaling pathway / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / peptidyl-tyrosine phosphorylation / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell junction / T cell receptor signaling pathway / adaptive immune response / cytoskeleton / intracellular signal transduction / lipid binding / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Tyrosine-protein kinase Tec, SH3 domain / Zinc finger, Btk motif / BTK motif / Zinc finger Btk-type profile. / Bruton's tyrosine kinase Cys-rich motif / SH3 Domains / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain ...Tyrosine-protein kinase Tec, SH3 domain / Zinc finger, Btk motif / BTK motif / Zinc finger Btk-type profile. / Bruton's tyrosine kinase Cys-rich motif / SH3 Domains / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / Src homology 3 domains / SH2 domain / SH3 type barrels. / 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. / PH-like domain superfamily / 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 Tec
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodSOLUTION NMR / ARIA
AuthorsMulhern, T.D. / Pursglove, S.E. / Booker, G.W.
CitationJournal: J. Biol. Chem. / Year: 2002
Title: The solution structure and intramolecular associations of the Tec kinase SRC homology 3 domain.
Authors: Pursglove, S.E. / Mulhern, T.D. / Mackay, J.P. / Hinds, M.G. / Booker, G.W.
History
DepositionAug 28, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYROSINE-PROTEIN KINASE TEC


Theoretical massNumber of molelcules
Total (without water)7,9091
Polymers7,9091
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 / 100LOWEST ENERGY
Representative

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Components

#1: Protein TYROSINE-PROTEIN KINASE TEC


Mass: 7908.657 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN (181-245)
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL GLY-SER FROM GLUTATHIONE S-TRANSFERASE FUSION PARTNER
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Description: GST-FUSION / Plasmid: PGEX-4T-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P24604, EC: 2.7.1.112
Sequence detailsN-TERMINAL GLY-SER FROM FUSION PARTNER

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
121TOCSY
131NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HETERONUCLEAR NMR SPECTROSCOPY ON 15N-LABELED SAMPLES

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Sample preparation

Sample conditionspH: 6.0 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: ARIA / Software ordinal: 1
Details: THESE COORDINATE SETS WERE REFINED IN EXPLICIT SOLVENT USING THE HYBRID CSDX/OPLS PARAMETER SET. DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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