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- PDB-2kuq: Solution structure of the chimera of the PTB domain of SNT-2 and ... -

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Basic information

Entry
Database: PDB / ID: 2kuq
TitleSolution structure of the chimera of the PTB domain of SNT-2 and 19-residue peptide (aa 1571-1589) of HALK
ComponentsFibroblast growth factor receptor substrate 3,LINKER,ALK tyrosine kinase receptor
KeywordsSIGNALING PROTEIN / Chimera / SNT-2 / PTB domain / hALK / Structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


response to environmental enrichment / 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 / receptor signaling protein tyrosine kinase activator activity / regulation of dopamine receptor signaling pathway ...response to environmental enrichment / 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 / receptor signaling protein tyrosine kinase activator activity / regulation of dopamine receptor signaling pathway / fibroblast growth factor receptor binding / ALK mutants bind TKIs / swimming behavior / transmembrane receptor protein tyrosine kinase adaptor activity / positive regulation of dendrite development / RND1 GTPase cycle / RND2 GTPase cycle / regulation of neuron differentiation / adult behavior / Signaling by ALK / Signaling by ALK fusions and activated point mutants / neuron development / fibroblast growth factor receptor signaling pathway / Activated NTRK2 signals through FRS2 and FRS3 / Nuclear events stimulated by ALK signaling in cancer / negative regulation of lipid catabolic process / energy homeostasis / peptidyl-tyrosine autophosphorylation / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / transmembrane receptor protein tyrosine kinase activity / hippocampus development / receptor protein-tyrosine kinase / cell surface receptor protein tyrosine kinase signaling pathway / heparin binding / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / RAF/MAP kinase cascade / protein tyrosine kinase activity / regulation of apoptotic process / protein autophosphorylation / receptor complex / phosphorylation / 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. / IRS-type PTB domain / PTB domain (IRS-1 type) / Glycine rich protein / Phosphotyrosine-binding domain / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. ...FRS2, PTB domain / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / Glycine rich protein / Phosphotyrosine-binding domain / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Concanavalin A-like lectin/glucanase domain superfamily / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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)
synthetic construct (others)
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model 1
AuthorsLi, H. / Koshiba, S. / Tomizawa, T. / Watanabe, S. / Harada, T. / 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 1.3Jan 15, 2020Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibroblast growth factor receptor substrate 3,LINKER,ALK tyrosine kinase receptor


Theoretical massNumber of molelcules
Total (without water)16,9541
Polymers16,9541
Non-polymers00
Water0
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,LINKER,ALK tyrosine kinase receptor / FGFR substrate 3 / FGFR-signaling adaptor SNT2 / Suc1-associated neurotrophic factor target 2 / SNT- ...FGFR substrate 3 / FGFR-signaling adaptor SNT2 / Suc1-associated neurotrophic factor target 2 / SNT-2 / Anaplastic lymphoma kinase


Mass: 16953.816 Da / Num. of mol.: 1 / Fragment: PTB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: FRS3, ALK / Production host: E. coli-cell-free protein synthesis / References: UniProt: O43559, UniProt: Q9UM73
Sequence detailsREISDUES 121-134 ARE LINKER

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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

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Sample preparation

DetailsContents: 1.12mM [U-13C; U-15N] (chain A)-1, 20mM [U-2H] TRIS-2, 100mM sodium chloride-3, 1mM [U-2H] DTT-4, 0.02% sodium azide-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.12 mM(chain A)-1[U-13C; U-15N]1
20 mMTRIS-2[U-2H]1
100 mMsodium chloride-31
1 mMDTT-4[U-2H]1
0.02 %sodium azide-51
Sample conditionsIonic strength: 120 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
NMRPipe20031121Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
KUJIRA0.982Kobayashi, N.data analysis
NMRViewJohnson, One Moon Scientificdata analysis
CYANA2.0.17Guntert, Mumenthaler and Wuthrichstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
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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