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- PDB-2ysz: Solution structure of the chimera of the C-terminal PID domain of... -

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Basic information

Entry
Database: PDB / ID: 2ysz
TitleSolution structure of the chimera of the C-terminal PID domain of Fe65L and the C-terminal tail peptide of APP
ComponentsAmyloid beta A4 precursor protein-binding family B member 2 and Amyloid beta A4 protein
KeywordsPROTEIN BINDING / Chimera / Fe65L / PID domain / amyloid precursor protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of cell cycle phase transition / Formyl peptide receptors bind formyl peptides and many other ligands / Advanced glycosylation endproduct receptor signaling / ECM proteoglycans / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / maintenance of lens transparency / TRAF6 mediated NF-kB activation / Lysosome Vesicle Biogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation ...negative regulation of cell cycle phase transition / Formyl peptide receptors bind formyl peptides and many other ligands / Advanced glycosylation endproduct receptor signaling / ECM proteoglycans / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / maintenance of lens transparency / TRAF6 mediated NF-kB activation / Lysosome Vesicle Biogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / TAK1-dependent IKK and NF-kappa-B activation / G alpha (q) signalling events / G alpha (i) signalling events / Platelet degranulation / Mitochondrial protein degradation / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / synaptic assembly at neuromuscular junction / axo-dendritic transport / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / mating behavior / regulation of spontaneous synaptic transmission / signaling receptor activator activity / Golgi-associated vesicle / ciliary rootlet / PTB domain binding / positive regulation of amyloid fibril formation / neuron remodeling / intracellular vesicle / nuclear envelope lumen / COPII-coated ER to Golgi transport vesicle / suckling behavior / dendrite development / modulation of excitatory postsynaptic potential / presynaptic active zone / neuromuscular process controlling balance / negative regulation of long-term synaptic potentiation / transition metal ion binding / smooth muscle contraction / regulation of multicellular organism growth / intracellular copper ion homeostasis / negative regulation of neuron differentiation / positive regulation of T cell migration / spindle midzone / smooth endoplasmic reticulum / protein serine/threonine kinase binding / forebrain development / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / positive regulation of G2/M transition of mitotic cell cycle / neuron projection maintenance / extracellular matrix organization / ionotropic glutamate receptor signaling pathway / positive regulation of mitotic cell cycle / positive regulation of calcium-mediated signaling / cholesterol metabolic process / axonogenesis / axon guidance / adult locomotory behavior / dendritic shaft / positive regulation of glycolytic process / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / locomotory behavior / long-term synaptic potentiation / positive regulation of JNK cascade / microglial cell activation / regulation of long-term neuronal synaptic plasticity / neuron migration / serine-type endopeptidase inhibitor activity / positive regulation of non-canonical NF-kappaB signal transduction / visual learning / neuromuscular junction / recycling endosome / neuron differentiation / memory / positive regulation of interleukin-6 production / cognition / neuron cellular homeostasis / positive regulation of inflammatory response / endocytosis / neuron projection development / cellular response to amyloid-beta / G2/M transition of mitotic cell cycle / positive regulation of tumor necrosis factor production / cell-cell junction / apical part of cell / synaptic vesicle / mitotic cell cycle / regulation of translation / heparin binding / amyloid-beta binding / growth cone / regulation of gene expression
Similarity search - Function
Amyloid beta precursor protein binding family B member 1/2/3 / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. ...Amyloid beta precursor protein binding family B member 1/2/3 / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Amyloid-beta precursor protein / Amyloid beta precursor protein binding family B member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLi, H. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure of the C-terminal phosphotyrosine interaction domain of Fe65L1 complexed with the cytoplasmic tail of amyloid precursor protein reveals a novel peptide binding mode
Authors: Li, H. / Koshiba, S. / Hayashi, F. / Tochio, N. / Tomizawa, T. / Kasai, T. / Yabuki, T. / Motoda, Y. / Harada, T. / Watanabe, S. / Inoue, M. / Hayashizaki, Y. / Tanaka, A. / Kigawa, T. / Yokoyama, S.
History
DepositionApr 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
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: Amyloid beta A4 precursor protein-binding family B member 2 and Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)20,0071
Polymers20,0071
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 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Amyloid beta A4 precursor protein-binding family B member 2 and Amyloid beta A4 protein


Mass: 20007.119 Da / Num. of mol.: 1 / Fragment: PID domain and APP peptide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: cell-free protein synthesis / Plasmid: P060710-04 / References: UniProt: Q9DBR4, UniProt: P12023

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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

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Sample preparation

DetailsContents: 1.00mM chimera sample U-15N, 13C; 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 / Pressure: ambient / Temperature: 296 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
XwinNMR3.5Brukercollection
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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