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- PDB-2rna: Itk SH3 average minimized -

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Basic information

Entry
Database: PDB / ID: 2rna
TitleItk SH3 average minimized
ComponentsTyrosine-protein kinase ITK/TSK
KeywordsTRANSFERASE / Itk / SH3 / beta barrel / 310 helix / regulatory / ATP-binding / Kinase / Membrane / Metal-binding / Nucleotide-binding / Phosphoprotein / SH2 domain / SH3 domain / Tyrosine-protein kinase / Zinc / Zinc-finger
Function / homology
Function and homology information


Generation of second messenger molecules / FCERI mediated Ca+2 mobilization / gamma-delta T cell activation / NK T cell differentiation / activation of phospholipase C activity / positive regulation of cytokine production / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cell-cell junction ...Generation of second messenger molecules / FCERI mediated Ca+2 mobilization / gamma-delta T cell activation / NK T cell differentiation / activation of phospholipase C activity / positive regulation of cytokine production / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cell-cell junction / T cell receptor signaling pathway / adaptive immune response / intracellular signal transduction / protein phosphorylation / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Tyrosine-protein kinase ITK, SH3 domain / Tyrosine-protein kinase ITK/TSK, catalytic 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. ...Tyrosine-protein kinase ITK, SH3 domain / Tyrosine-protein kinase ITK/TSK, catalytic 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 ITK/TSK
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsSeverin, A.J.
CitationJournal: To be Published
Title: NMR structure note: murine Itk SH3 domain
Authors: Severin, A.J. / Fulton, D.B. / Andreotti, A.H.
History
DepositionDec 8, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase ITK/TSK


Theoretical massNumber of molelcules
Total (without water)7,4701
Polymers7,4701
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)1 / -
Representativeminimized average structure

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Components

#1: Protein Tyrosine-protein kinase ITK/TSK / T-cell-specific kinase / IL-2-inducible T-cell kinase / Kinase EMT / Kinase TLK


Mass: 7470.039 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itk, Emt, Tlk, Tsk / Plasmid: pgex2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q03526, non-specific protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 15N 1H HSQC, CBCA(CO)CH, HN(CA)CB, HBHA(CO)NH, HBHANH, HNCO, (HB)CB(CGCDCE)HE, (HB)CB(CGCD)HD, (H)CCH-TOCSY, 3D 15N-edited TOCSY, 2D homonuclear TOCSY, 2D homonuclear NOESY, 3D 13C-edited ...Type: 15N 1H HSQC, CBCA(CO)CH, HN(CA)CB, HBHA(CO)NH, HBHANH, HNCO, (HB)CB(CGCDCE)HE, (HB)CB(CGCD)HD, (H)CCH-TOCSY, 3D 15N-edited TOCSY, 2D homonuclear TOCSY, 2D homonuclear NOESY, 3D 13C-edited aliphatic NOESY, 3D 13C-edited aromatic NOESY, 15N-edited NOESY, 15N-edited TOCSY, IPAP 1H-15N, J correlation HNHA, long range coupling HNCO hydrogen bond experiment

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Sample preparation

DetailsContents: 3.4mM [U-100% 13C; U-100% 15N] Itk Sh3, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 3.4 mM / Component: Itk Sh3 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 75mM NaCl / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVII / Manufacturer: Bruker / Model: AVII / Field strength: 700.133 MHz

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Processing

NMR softwareName: CNS / Developer: Schwieters, Kuszewski, Tjandra and Clore / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Xplor-NIH refine.py script
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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