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- PDB-2lmj: Itk-sh3 -

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Basic information

Entry
Database: PDB / ID: 2lmj
TitleItk-sh3
ComponentsTyrosine-protein kinase ITK/TSK
KeywordsTRANSFERASE
Function / homology
Function and homology information


gamma-delta T cell activation / NK T cell differentiation / activation of phospholipase C activity / Generation of second messenger molecules / cellular defense response / T cell activation / FCERI mediated Ca+2 mobilization / positive regulation of cytokine production / B cell receptor signaling pathway / non-specific protein-tyrosine kinase ...gamma-delta T cell activation / NK T cell differentiation / activation of phospholipase C activity / Generation of second messenger molecules / cellular defense response / T cell activation / FCERI mediated Ca+2 mobilization / 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 / phosphorylation / signal transduction / 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 / 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. / 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsKristiansen, P. / Bie Andersen, T. / Huszenicza, Z. / Andreotti, A.H. / Spurkland, A.
CitationJournal: To be Published
Title: The SH3 domains of the Tec family kinase Itk and the Src family kinase Lck compete for adjacent sites on T-cell specific adapter protein
Authors: Bie Andersen, T. / Kristiansen, P. / Huszenicza, Z. / Andreotti, A.H. / Spurkland, A.
History
DepositionDec 5, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 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 / struct_ref_seq_dif
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 / _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)7,6581
Polymers7,6581
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 7658.336 Da / Num. of mol.: 1 / Fragment: SH3 domain residues 171-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITK, EMT, LYK / Production host: Escherichia coli (E. coli) / Strain (production host): bl21
References: UniProt: Q08881, non-specific protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D HNCO
1513D CBCA(CO)NH
1613D HNCA
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D HN(CO)CA
11013D HBHANH
11113D HN(CA)CO
11213D C(CO)NH
11313D H(CCO)NH
11412D 1H-13C HSQC
11522D 1H-13C HSQC
11623D (H)CCH-TOCSY
11723D CCH-TOCSY
11823D 1H-13C NOESY
21912D 1H-15N HSQC
32012D 1H-15N HSQC
42112D 1H-15N HSQC
52212D 1H-15N HSQC
62312D 1H-15N HSQC
12411H
12521H

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-98% 13C; U-98% 15N] ITK-SH3, 95 % H2O, 5 % 98% D2O, 0.2 mM DSS, 20 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
21.0 mM [U-98% 13C; U-98% 15N] ITK-SH3, 100 % 99.98 D2O, 0.2 mM DSS, 20 mM potassium phosphate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMITK-SH3-1[U-98% 13C; U-98% 15N]1
95 %H2O-21
5 %D2O-398%1
.2 mMDSS-41
20 mMpotassium phosphate-51
1.0 mMITK-SH3-6[U-98% 13C; U-98% 15N]2
100 %D2O-799.982
.2 mMDSS-82
20 mMpotassium phosphate-92
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 6.5 ambient 298 K
220 6.5 ambient 293 K
320 6.5 ambient 288 K
420 6.5 ambient 283 K
520 6.5 ambient 303 K
620 6.5 ambient 308 K

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NMR measurement

NMR spectrometerType: Bruker Avance II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
Sparky3.114T. D. Goddard and D. G. Kneller,chemical shift assignment
CARA1Fred Dambergerchemical shift assignment
CARA1Fred Dambergerpeak picking
TALOS+Cornilescu, Delaglio and Baxdata analysis
TopSpin2.1p4Bruker Biospincollection
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1286 / Hydrogen bond constraints total count: 84 / Protein phi angle constraints total count: 40 / Protein psi angle constraints total count: 40
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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