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- PDB-2k7a: Ensemble Structures of the binary complex between the SH3 and SH2... -

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Basic information

Entry
Database: PDB / ID: 2k7a
TitleEnsemble Structures of the binary complex between the SH3 and SH2 domain of interleukin-2 tyrosine kinase.
Components
  • SH2 domain of Tyrosine-protein kinase ITK/TSK
  • SH3 domain of Tyrosine-protein kinase ITK/TSK
KeywordsTRANSFERASE / SH3 / SH2 / novel / cis / ATP-binding / Cell membrane / 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 / NK T cell differentiation / gamma-delta T cell activation / positive regulation of cytokine production / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / cell-cell junction / T cell receptor signaling pathway / adaptive immune response ...Generation of second messenger molecules / FCERI mediated Ca+2 mobilization / NK T cell differentiation / gamma-delta T cell activation / positive regulation of cytokine production / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / cell-cell junction / T cell receptor signaling pathway / adaptive immune response / protein phosphorylation / intracellular signal transduction / zinc ion binding / ATP binding / nucleus / 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 / SH2 domain / SHC Adaptor Protein / SH3 Domains / PH 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 / SH2 domain / SHC Adaptor Protein / 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 / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase ITK/TSK
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsAndreotti, A.H. / Severin, A.J. / Fulton, D.B.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Proline isomerization preorganizes the Itk SH2 domain for binding to the Itk SH3 domain.
Authors: Severin, A. / Joseph, R.E. / Boyken, S. / Fulton, D.B. / Andreotti, A.H.
History
DepositionAug 8, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 1, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.3May 1, 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

Downloads & links

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Assembly

Deposited unit
A: SH3 domain of Tyrosine-protein kinase ITK/TSK
B: SH2 domain of Tyrosine-protein kinase ITK/TSK


Theoretical massNumber of molelcules
Total (without water)20,0342
Polymers20,0342
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1470 Å2
ΔGint-6 kcal/mol
Surface area9600 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein SH3 domain of Tyrosine-protein kinase ITK/TSK / T-cell-specific kinase / IL-2-inducible T-cell kinase / Kinase EMT / Kinase TLK


Mass: 7355.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itk, Emt, Tlk, Tsk / Production host: Escherichia coli (E. coli)
References: UniProt: Q03526, non-specific protein-tyrosine kinase
#2: Protein SH2 domain of Tyrosine-protein kinase ITK/TSK / T-cell-specific kinase / IL-2-inducible T-cell kinase / Kinase EMT / Kinase TLK


Mass: 12678.335 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itk, Emt, Tlk, Tsk / Production host: Escherichia coli (E. coli)
References: UniProt: Q03526, 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 CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-15N TOCSY
11013D 1H-13C NOESY
11112D 1H-15N IPAP
11213D HNCA COSY
11312D 1H-15N IPAP
11413D HNCA COSY
1151(HB)CB(CGCDCE)HE
1161(HB)CB(CGCD)HD
11722D 1H-15N HSQC
11822D 1H-13C HSQC
11923D CBCA(CO)NH
12023D HNCO
12123D HN(CA)CB
12223D HN(CA)CB
12323D HBHA(CO)NH
12423D (H)CCH-TOCSY
12523D 1H-15N NOESY
12623D 1H-15N TOCSY
12723D 1H-13C NOESY
12822D 1H-15N IPAP
12922D 1H-15N IPAP
1302(HB)CB(CGCDCE)HE
1312(HB)CB(CGCD)HD
13222D 1H-15N HSQC
13332D 1H-15N HSQC
13442D 1H-15N HSQC
13532D 1H-13C HSQC
13642D 1H-13C HSQC
13733D CBCA(CO)NH
13843D CBCA(CO)NH
13933D HNCO
14043D HNCO
14133D HNHA
14243D HNHA
14333D HN(CA)CB
14443D HN(CA)CB
14533D 1H-15N NOESY
14643D 1H-15N NOESY
14733D 1H-15N TOCSY
14843D 1H-15N TOCSY
14933D 1H-13C NOESY
15043D 1H-13C NOESY
1513(HB)CB(CGCD)HD
1524(HB)CB(CGCD)HD
1533(HB)CB(CGCDCE)HE
1544(HB)CB(CGCDCE)HE
15532D 1H-15N IPAP
15642D 1H-15N IPAP
15743D HNCA COSY
15843D HNCA COSY
15932D 1H-15N IPAP
16042D 1H-15N IPAP
16133D HBHA(CO)NH
16243D HBHA(CO)NH
16333D (H)CCH-TOCSY
16443D (H)CCH-TOCSY
16532D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
13.4 mM [U-100% 13C; U-100% 15N] Itk SH3 domain, 1.5 mM Itk SH2 domain, 95% H2O/5% D2O95% H2O/5% D2O
23.4 mM [U-100% 13C; U-100% 15N] Itk SH2 domain, 1.5 mM Itk SH3 domain, 95% H2O/5% D2O95% H2O/5% D2O
31.5 mM [U-100% 13C; U-100% 15N] Itk SH2 domain, 3.4 mM Itk SH3 domain, 95% H2O/5% D2O95% H2O/5% D2O
41.5 mM [U-100% 13C; U-100% 15N] Itk SH3 domain, 3.4 mM Itk SH2 domain, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3.4 mMItk SH3 domain[U-100% 13C; U-100% 15N]1
1.5 mMItk SH2 domain1
3.4 mMItk SH2 domain[U-100% 13C; U-100% 15N]2
1.5 mMItk SH3 domain2
1.5 mMItk SH2 domain[U-100% 13C; U-100% 15N]3
3.4 mMItk SH3 domain3
1.5 mMItk SH3 domain[U-100% 13C; U-100% 15N]4
3.4 mMItk SH2 domain4
Sample conditionsIonic strength: 75 / 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 MHz

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Processing

NMR software
NameVersionDeveloperClassification
xplor-nih2.19Brunger A. T. et.al.refinement
CARA1.8.4Keller and Wuthrichchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: refine.py script from xplor-nih 2.19
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 60 / Conformers submitted total number: 20 / Representative conformer: 1

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