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- PDB-2roz: Structure of the C-terminal PID Domain of Fe65L1 Complexed with t... -

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Basic information

Entry
Database: PDB / ID: 2roz
TitleStructure of the C-terminal PID Domain of Fe65L1 Complexed with the Cytoplasmic Tail of APP Reveals a Novel Peptide Binding Mode
Components
  • Amyloid beta A4 precursor protein-binding family B member 2
  • peptide from Amyloid beta A4 protein
KeywordsPEPTIDE BINDING PROTEIN / Fe65L1 / PID domain / amyloid precursor protein / Alternative splicing / Amyloid / Apoptosis / Cell adhesion / Coated pit / Copper / Endocytosis / Glycoprotein / Heparin-binding / Iron / Membrane / Metal-binding / Notch signaling pathway / Phosphoprotein / Protease inhibitor / Serine protease inhibitor / Transmembrane / Zinc / 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 / negative regulation of presynapse assembly / Advanced glycosylation endproduct receptor signaling / cytosolic mRNA polyadenylation / ECM proteoglycans / synaptic assembly at neuromuscular junction / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / maintenance of lens transparency / TRAF6 mediated NF-kB activation ...negative regulation of cell cycle phase transition / Formyl peptide receptors bind formyl peptides and many other ligands / negative regulation of presynapse assembly / Advanced glycosylation endproduct receptor signaling / cytosolic mRNA polyadenylation / ECM proteoglycans / synaptic assembly at neuromuscular junction / 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 / smooth endoplasmic reticulum calcium ion homeostasis / TAK1-dependent IKK and NF-kappa-B activation / G alpha (q) signalling events / G alpha (i) signalling events / Platelet degranulation / ciliary rootlet / Mitochondrial protein degradation / suckling behavior / COPII-coated ER to Golgi transport vesicle / collateral sprouting in absence of injury / regulation of synapse structure or activity / axo-dendritic transport / axon midline choice point recognition / central nervous system neuron differentiation / presynaptic active zone / mating behavior / neuromuscular process controlling balance / Golgi-associated vesicle / neuron remodeling / negative regulation of neuron differentiation / spindle midzone / intracellular vesicle / forebrain development / dendrite development / smooth endoplasmic reticulum / signaling receptor activator activity / transition metal ion binding / smooth muscle contraction / regulation of multicellular organism growth / intracellular copper ion homeostasis / positive regulation of G2/M transition of mitotic cell cycle / cholesterol metabolic process / clathrin-coated pit / Notch signaling pathway / extracellular matrix organization / ionotropic glutamate receptor signaling pathway / axonogenesis / positive regulation of mitotic cell cycle / axon guidance / adult locomotory behavior / locomotory behavior / neuromuscular junction / serine-type endopeptidase inhibitor activity / neuron cellular homeostasis / visual learning / recycling endosome / G2/M transition of mitotic cell cycle / memory / cognition / long-term synaptic potentiation / neuron differentiation / endocytosis / neuron migration / neuron projection development / apical part of cell / synaptic vesicle / cell-cell junction / mitotic cell cycle / heparin binding / regulation of gene expression / regulation of translation / amyloid-beta binding / growth cone / response to oxidative stress / neuron apoptotic process / cytoplasmic vesicle / perikaryon / gene expression / early endosome / neuron projection / receptor complex / cell adhesion / protein stabilization / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / axon / protein domain specific binding / protein kinase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular region / identical protein binding
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. / Tochio, N. / Watanabe, S. / Harada, T. / Inoue, M. / 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 25, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 22, 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:
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Assembly

Deposited unit
A: peptide from Amyloid beta A4 protein
B: Amyloid beta A4 precursor protein-binding family B member 2


Theoretical massNumber of molelcules
Total (without water)18,5872
Polymers18,5872
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide peptide from Amyloid beta A4 protein / APP-derived_32-mer_peptide


Mass: 3836.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICAL SYNTHESIS / References: UniProt: P12023
#2: Protein Amyloid beta A4 precursor protein-binding family B member 2 / Fe65L1


Mass: 14750.546 Da / Num. of mol.: 1 / Fragment: C-terminal PID Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: E. COLI CELL-FREE / Gene: Apbb2 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: Q9DBR4

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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 F3-EDITED NOESY
1413D 13C,15N F1-FILTERED 15N F3-EDITED NOESY
1512D F2 13C,15N- FILTERED NOESY
NMR detailsText: The experiments of the conventional NOESY spectra, 3D 1H-15N NOESY and 3D 1H-13C NOESY, are conducted at 900 MHZ BRUKER AVANCE machine. However, the other three filter-related experiments, 3D_ ...Text: The experiments of the conventional NOESY spectra, 3D 1H-15N NOESY and 3D 1H-13C NOESY, are conducted at 900 MHZ BRUKER AVANCE machine. However, the other three filter-related experiments, 3D_13C,15N F1-FILTERED 13C F3-EDITED NOESY, 3D_13C,15N F1-FILTERED 15N F3-EDITED NOESY, and 2D_F2 13C,15N- FILTERED NOESY, are conducted at 800 MHZ BRUKER AVANCE machine.

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Sample preparation

DetailsContents: 0.37mM [U-13C; U-15N] Fe65L1 PID2, 0.37mM APP-derived 32-mer peptide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.37 mMFe65L1 PID2[U-13C; U-15N]1
0.37 mMAPP-derived 32-mer peptide1
Sample conditionsIonic strength: 0.12 / 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, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.0.4Johnson, One Moon Scientificdata analysis
KUJIRA0.982Kobayashi, N.data analysis
CYANA1.0.8Herrmann, Guntert and Wuthrichstructure solution
CYANA1.0.8Herrmann, Guntert and Wuthrichrefinement
RefinementMethod: torsion angle 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 / Representative conformer: 1

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