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- PDB-2kk6: Solution structure of sh2 domain of proto-oncogene tyrosine-prote... -

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Basic information

Entry
Database: PDB / ID: 2kk6
TitleSolution structure of sh2 domain of proto-oncogene tyrosine-protein kinase fer from homo sapiens, northeast structural genomics consortium (nesg) target hr3461d
ComponentsProto-oncogene tyrosine-protein kinase FER
KeywordsTRANSFERASE / methods development / SH2 / Proto-oncogene tyrosine-protein kinase FER / NESG / ATP-binding / Cytoplasm / Kinase / Nucleotide-binding / Nucleus / Phosphoprotein / Polymorphism / Proto-oncogene / SH2 domain / Tyrosine-protein kinase / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


adherens junction disassembly / response to platelet-derived growth factor / diapedesis / extracellular matrix-cell signaling / negative regulation of mast cell activation involved in immune response / regulation of fibroblast migration / regulation of epidermal growth factor receptor signaling pathway / Kit signaling pathway / cellular response to macrophage colony-stimulating factor stimulus / Sertoli cell development ...adherens junction disassembly / response to platelet-derived growth factor / diapedesis / extracellular matrix-cell signaling / negative regulation of mast cell activation involved in immune response / regulation of fibroblast migration / regulation of epidermal growth factor receptor signaling pathway / Kit signaling pathway / cellular response to macrophage colony-stimulating factor stimulus / Sertoli cell development / cell-cell adhesion mediated by cadherin / protein phosphatase 1 binding / adherens junction assembly / tyrosine phosphorylation of STAT protein / regulation of lamellipodium assembly / epidermal growth factor receptor binding / interleukin-6-mediated signaling pathway / positive regulation of actin filament polymerization / seminiferous tubule development / germ cell development / Fc-epsilon receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / substrate adhesion-dependent cell spreading / cell projection / adherens junction / non-specific protein-tyrosine kinase / regulation of protein phosphorylation / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / microtubule cytoskeleton organization / cellular response to reactive oxygen species / peptidyl-tyrosine phosphorylation / chemotaxis / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / cell cortex / actin cytoskeleton organization / protein tyrosine kinase activity / response to lipopolysaccharide / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / cell adhesion / intracellular signal transduction / positive regulation of cell migration / protein phosphorylation / lipid binding / positive regulation of cell population proliferation / chromatin / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tyrosine-protein kinase Fer, F-BAR domain / Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH2 domain ...Tyrosine-protein kinase Fer, F-BAR domain / Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH2 domain / SHC Adaptor Protein / : / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase Fer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsfewest violations, model 1
AuthorsTang, Y. / Wang, D. / Nwosu, C. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. ...Tang, Y. / 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: To be Published
Title: Solution structure of sh2 domain of proto-oncogene tyrosine-protein kinase fer from homo sapiens, northeast structural genomics consortium (nesg) target hr3461d
Authors: Tang, Y. / Montelione, G.T.
History
DepositionJun 15, 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 1.3May 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

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase FER


Theoretical massNumber of molelcules
Total (without water)13,6461
Polymers13,6461
Non-polymers00
Water00
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 Proto-oncogene tyrosine-protein kinase FER / c-FER / p94-FER / Tyrosine kinase 3


Mass: 13645.578 Da / Num. of mol.: 1 / Fragment: SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FER, TYK3 / Production host: Escherichia coli (E. coli)
References: UniProt: P16591, 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
1222D 1H-13C HSQC
1323D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D HBHA(CO)NH
1713D C(CO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.03 mM [U-100% 13C; U-100% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
21.20 mM [U-10% 13C; U-100% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.03 mMprotein-1[U-100% 13C; U-100% 15N]1
1.20 mMprotein-2[U-10% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
Sparky2.1Goddarddata analysis
Sparky2.1Goddardchemical shift assignment
Sparky2.1Goddardpeak picking
NMRPipe2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin2.1Bruker Biospincollection
RefinementMethod: simulated annealing, molecular dynamics / 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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