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- PDB-2eu0: The NMR ensemble structure of the Itk SH2 domain bound to a phosp... -

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Basic information

Entry
Database: PDB / ID: 2eu0
TitleThe NMR ensemble structure of the Itk SH2 domain bound to a phosphopeptide
Components
  • Lymphocyte cytosolic protein 2 phosphopeptide fragment
  • Tyrosine-protein kinase ITK/TSK
KeywordsTRANSFERASE / cis/trans isomerization / interleukin-2 tyrosine kinase / Itk / t-cell specific kinase / tsk / src homology 2 / SH2 / proline / phosphotyrosine binding
Function / homology
Function and homology information


TCR signalosome / GPVI-mediated activation cascade / FCERI mediated MAPK activation / Generation of second messenger molecules / mast cell activation / FCERI mediated Ca+2 mobilization / NK T cell differentiation / gamma-delta T cell activation / DAP12 signaling / plasma membrane raft ...TCR signalosome / GPVI-mediated activation cascade / FCERI mediated MAPK activation / Generation of second messenger molecules / mast cell activation / FCERI mediated Ca+2 mobilization / NK T cell differentiation / gamma-delta T cell activation / DAP12 signaling / plasma membrane raft / 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 / SAM domain (Sterile alpha motif) ...: / 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 / SAM domain (Sterile alpha motif) / Sterile alpha motif. / PH domain / : / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / 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 / 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 / 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 / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase ITK/TSK / Lymphocyte cytosolic protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / Distance geometry simulated annealing was used for refinement
AuthorsSundd, M. / Pletneva, E.V. / Fulton, D.B. / Andreotti, A.H.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Molecular Details of Itk Activation by Prolyl Isomerization and Phospholigand Binding: The NMR Structure of the Itk SH2 Domain Bound to a Phosphopeptide.
Authors: Pletneva, E.V. / Sundd, M. / Fulton, D.B. / Andreotti, A.H.
#1: Journal: Nat.Struct.Biol. / Year: 2002
Title: Structural characterization of a proline-driven conformational switch within the Itk SH2 domain
Authors: Mallis, R.J. / Brazin, K.N. / Fulton, D.B. / Andreotti, A.H.
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase ITK/TSK
B: Lymphocyte cytosolic protein 2 phosphopeptide fragment


Theoretical massNumber of molelcules
Total (without water)13,3552
Polymers13,3552
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 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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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 / Itk


Mass: 12560.243 Da / Num. of mol.: 1 / Fragment: SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itk, Emt, Tlk, Tsk / Plasmid: pGEX(2T) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03526, EC: 2.7.1.112
#2: Protein/peptide Lymphocyte cytosolic protein 2 phosphopeptide fragment / SH2 domain-containing leucocyte protein of 76 kDa / SLP-76 tyrosine phosphoprotein / SLP76


Mass: 794.723 Da / Num. of mol.: 1
Fragment: phosphopeptide fragment, sequence database residues 143-148
Source method: obtained synthetically
Details: This sequence occurs naturally in Mus musculus (mouse)
References: UniProt: Q60787
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
132HNHA
1433D 13C-separated NOESY
1533D 13C separated aromatic NOESY
163HN(CA)CB
173CBCA(CO)NH
183(H)CCH TOCSY
193C(CO)NH
110313C edited 13C/15 N filtered NOESY
111315N edited 13C/15N filtered NOESY
11242D TOCSY
1135D2O exchange experiment

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM Itk SH2 domain, 20mM phosphopeptide, 50mM KH2PO4, 75mM NaCl, 2mM DTT, 0.02% NaN3, pH 7.490% H2O/10% D2O
2U-15N labeled, 1mM Itk SH2 domain, 20mM phosphopeptide, 50mM KH2PO4, 75mM NaCl, 2mM DTT, 0.02% NaN3, pH 7.490% H2O/10% D2O
3U-15N, 13-C labeled, 1mM Itk SH2 domain, 20mM phosphopeptide, 50mM KH2PO4, 75mM NaCl, 2mM DTT, 0.02% NaN3, pH 7.490% H2O/10% D2O
45mM phosphopeptide, 50mM KH2PO4, 75mM NaCl, 2mM DTT, 0.02% NaN3, pH 7.490%H20, 10%D2O
51mM Itk SH2 domain, 20mM phosphopeptide, 50mM KH2PO4, 75mM NaCl, 2mM DTT, 0.02% NaN3, pH 7.4100% D2O
Sample conditionsIonic strength: 125mM / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRcollection
NMRPipeDelaglio et alprocessing
NMRView4.1.3Johnson and Blevinsdata analysis
CNS1Brunger et alrefinement
RefinementMethod: Distance geometry simulated annealing was used for refinement
Software ordinal: 1
Details: 2486 Intramolecular NOE restraints, 31 intermolecular NOE restraints, 63 dihedral angles calculated using HNHA experiment and TALOS and 27 hydrogen bonds (D20 exchange based restraints)
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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