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- PDB-2ys5: Solution structure of the complex of the PTB domain of SNT-2 and ... -

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Basic information

Entry
Database: PDB / ID: 2ys5
TitleSolution structure of the complex of the PTB domain of SNT-2 and 19-residue peptide (aa 1571-1589) of hALK
Components
  • ALK tyrosine kinase receptor
  • Fibroblast growth factor receptor substrate 3
KeywordsSIGNALING PROTEIN / Complex / 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


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 / 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 / neuron development / fibroblast growth factor receptor signaling pathway / Activated NTRK2 signals through FRS2 and FRS3 / 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 / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by ALK fusions and activated point mutants / receptor protein-tyrosine kinase / heparin binding / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / RAF/MAP kinase cascade / regulation of apoptotic process / protein tyrosine kinase activity / 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 / Tyrosine protein kinases specific active-site signature. / Concanavalin A-like lectin/glucanase domain superfamily / 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)
MethodSOLUTION NMR / torsion angle dynamics
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
DepositionApr 3, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,6762
Polymers18,6762
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 / 100structures with the least restraint violations, target function
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) / Description: cell-free protein synthesis / Gene: FRS3 / Plasmid: P060320-18 / References: UniProt: O43559
#2: Protein/peptide ALK tyrosine kinase receptor / Anaplastic lymphoma kinase / CD246 antigen


Mass: 2343.644 Da / Num. of mol.: 1 / Fragment: residues in database 1571-1589 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence is taken from Homo sapiens.
References: UniProt: Q9UM73, receptor protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated 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 SNT-2 PTB domain U-15N, 13C in complex with hALK peptide (1:1); 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / 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
XwinNMR3.5Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.982Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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