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- PDB-2kk1: Solution structure of C-terminal Domain of Tyrosine-protein kinas... -

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Basic information

Entry
Database: PDB / ID: 2kk1
TitleSolution structure of C-terminal Domain of Tyrosine-protein kinase ABL2 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) target HR5537A
ComponentsTyrosine-protein kinase ABL2
KeywordsTRANSFERASE / Methods development / Tyrosin protein kinase abl2 / F-actin binding domain / NESG / Alternative splicing / ATP-binding / Cell adhesion / Cytoplasm / Cytoskeleton / Kinase / Lipoprotein / Magnesium / Manganese / Metal-binding / Myristate / Nucleotide-binding / Phosphoprotein / Polymorphism / SH2 domain / SH3 domain / Tyrosine-protein kinase / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


positive regulation of oxidoreductase activity / Role of ABL in ROBO-SLIT signaling / regulation of cell motility / exploration behavior / negative regulation of Rho protein signal transduction / regulation of endocytosis / actin monomer binding / RAC3 GTPase cycle / positive regulation of T cell migration / regulation of cell adhesion ...positive regulation of oxidoreductase activity / Role of ABL in ROBO-SLIT signaling / regulation of cell motility / exploration behavior / negative regulation of Rho protein signal transduction / regulation of endocytosis / actin monomer binding / RAC3 GTPase cycle / positive regulation of T cell migration / regulation of cell adhesion / : / cellular response to retinoic acid / Negative regulation of FLT3 / RAC1 GTPase cycle / positive regulation of establishment of T cell polarity / phosphotyrosine residue binding / regulation of autophagy / regulation of actin cytoskeleton organization / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / protein modification process / epidermal growth factor receptor signaling pathway / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / actin filament binding / actin cytoskeleton / manganese ion binding / positive regulation of cytosolic calcium ion concentration / regulation of apoptotic process / protein tyrosine kinase activity / cell adhesion / protein kinase activity / magnesium ion binding / signal transduction / ATP binding / cytosol
Similarity search - Function
Nucleotidyltransferases domain 2 / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains ...Nucleotidyltransferases domain 2 / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Tyrosine-protein kinase ABL2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics, simulated annealing, distance geometry
Model detailsfewest violations, model 1
AuthorsLiu, G. / Wang, D. / Nwosu, C. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. ...Liu, G. / Wang, D. / Nwosu, C. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2010
Title: NMR structure of F-actin-binding domain of Arg/Abl2 from Homo sapiens.
Authors: Liu, G. / Huang, Y.J. / Xiao, R. / Wang, D. / Acton, T.B. / Montelione, G.T.
History
DepositionJun 14, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase ABL2


Theoretical massNumber of molelcules
Total (without water)14,5571
Polymers14,5571
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Tyrosine-protein kinase ABL2 / Abelson murine leukemia viral oncogene homolog 2 / Abelson-related gene protein / Tyrosine kinase ARG


Mass: 14557.477 Da / Num. of mol.: 1 / Fragment: sequence database residues 1058-1182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL2, ABLL, ARG / Production host: Escherichia coli (E. coli)
References: UniProt: P42684, 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
1232D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1623D 1H-13C NOESY
1713D HBHA(CO)NH
1813D C(CO)NH
1913D (H)CCH-TOCSY
11013D 1H-13C-15N simutaneous NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-100% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
21.2 mM [U-100% 13C; U-100% 15N] protein, 100% D2O100% D2O
31.2 mM [U-10% 13C; U-100% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMprotein-1[U-100% 15N]1
1.2 mMprotein-2[U-100% 13C; U-100% 15N]2
1.2 mMprotein-3[U-10% 13C; U-100% 15N]3
Sample conditionsIonic strength: 0.2 / pH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
XEASY1.3Bartels et al.chemical shift assignment
XEASY1.3Bartels et al.data analysis
XEASY1.3Bartels et al.peak picking
NMRPipe1.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VnmrJ1.3Variancollection
TopSpin1.3Bruker Biospincollection
RefinementMethod: molecular dynamics, simulated annealing, distance geometry
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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