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- PDB-2kup: Solution structure of the complex of the PTB domain of SNT-2 and ... -

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Basic information

Entry
Database: PDB / ID: 2kup
TitleSolution structure of the complex of the PTB domain of SNT-2 and 19-residue peptide (aa 1571-1589) of HALK
Components
  • 19-residue peptide from ALK tyrosine kinase receptor
  • Fibroblast growth factor receptor substrate 3
KeywordsSIGNALING PROTEIN/ONCOPROTEIN / Complex / SNT-2 / PTB DOMAIN / hALK / structural genomics / signaling protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / SIGNALING PROTEIN-ONCOPROTEIN complex
Function / homology
Function and homology information


ASP-3026-resistant ALK mutants / NVP-TAE684-resistant ALK mutants / alectinib-resistant ALK mutants / brigatinib-resistant ALK mutants / ceritinib-resistant ALK mutants / crizotinib-resistant ALK mutants / lorlatinib-resistant ALK mutants / MDK and PTN in ALK signaling / receptor signaling protein tyrosine kinase activator activity / regulation of dopamine receptor signaling pathway ...ASP-3026-resistant ALK mutants / NVP-TAE684-resistant ALK mutants / alectinib-resistant ALK mutants / brigatinib-resistant ALK mutants / ceritinib-resistant ALK mutants / crizotinib-resistant ALK mutants / lorlatinib-resistant ALK mutants / MDK and PTN in ALK signaling / receptor signaling protein tyrosine kinase activator activity / regulation of dopamine receptor signaling pathway / response to environmental enrichment / fibroblast growth factor receptor binding / ALK mutants bind TKIs / transmembrane receptor protein tyrosine kinase adaptor activity / swimming behavior / RND1 GTPase cycle / regulation of neuron differentiation / RND2 GTPase cycle / positive regulation of dendrite development / Signaling by ALK / phosphorylation / response to stress / adult behavior / fibroblast growth factor receptor signaling pathway / neuron development / Activated NTRK2 signals through FRS2 and FRS3 / negative regulation of lipid catabolic process / peptidyl-tyrosine autophosphorylation / FRS-mediated FGFR3 signaling / energy homeostasis / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / hippocampus development / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / positive regulation of NF-kappaB transcription factor activity / Signaling by ALK fusions and activated point mutants / heparin binding / regulation of cell population proliferation / RAF/MAP kinase cascade / protein autophosphorylation / protein tyrosine kinase activity / regulation of apoptotic process / receptor complex / signal transduction / protein-containing complex / extracellular exosome / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
FRS2, PTB domain / : / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / : / ALK/LTK, Glycine-rich domain / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / MAM domain, meprin/A5/mu ...FRS2, PTB domain / : / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / : / ALK/LTK, Glycine-rich domain / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / PH-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / 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 / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor receptor substrate 3 / ALK tyrosine kinase receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model 1
AuthorsLi, H. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Struct.Funct.Genom. / Year: 2010
Title: Structural basis for the recognition of nucleophosmin-anaplastic lymphoma kinase oncoprotein by the phosphotyrosine binding domain of Suc1-associated neurotrophic factor-induced tyrosine-phosphorylated target-2
Authors: Koshiba, S. / Li, H. / Motoda, Y. / Tomizawa, T. / Kasai, T. / Tochio, N. / Yabuki, T. / Harada, T. / Watanabe, S. / Tanaka, A. / Shirouzu, M. / Kigawa, T. / Yamamoto, T. / Yokoyama, S.
History
DepositionFeb 24, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3May 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
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

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Assembly

Deposited unit
A: Fibroblast growth factor receptor substrate 3
B: 19-residue peptide from ALK tyrosine kinase receptor


Theoretical massNumber of molelcules
Total (without water)18,6762
Polymers18,6762
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 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Fibroblast growth factor receptor substrate 3 / FGFR substrate 3 / Suc1-associated neurotrophic factor target 2 / SNT-2 / FGFR-signaling adaptor SNT2


Mass: 16332.278 Da / Num. of mol.: 1 / Fragment: PTB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: cell-free synthesis (others) / References: UniProt: O43559
#2: Protein/peptide 19-residue peptide from ALK tyrosine kinase receptor / HALK / Anaplastic lymphoma kinase


Mass: 2343.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized / References: UniProt: Q9UM73

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D 13C,15N-F1 FILTERED 13C-EDITED NOESY
1413D 13C,15N-F1 FILTERED 15N-EDITED NOESY
1512D F2-13C FILTERED NOESY

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Sample preparation

DetailsContents: 0.37mM [U-13C; U-15N] (SNT-2 PTB domain)-1, 0.37mM (hALK peptide)-2, 20mM [U-2H] TRIS-3, 100mM sodium chloride-4, 1mM [U-2H] DTT-5, 0.02% sodium azide-6, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.37 mMSNT-2 PTB domain-1[U-13C; U-15N]1
0.37 mMhALK peptide-21
20 mMTRIS-3[U-2H]1
100 mMsodium chloride-41
1 mMDTT-5[U-2H]1
0.02 %sodium azide-61
Sample conditionsIonic strength: 120 / pH: 7 / 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
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmstructure solution
XwinNMR3.5Bruker Biospincollection
NMRPipe20031121Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.0.4Johnson, One Moon Scientificdata analysis
KUJIRA0.982Kobayashi, N.data analysis
CYANA2.0.17Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.0.17Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Representative conformer: 1

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