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- PDB-2yt0: Solution structure of the chimera of the C-terminal tail peptide ... -
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Basic information
Entry | Database: PDB / ID: 2yt0 | ||||||
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Title | Solution structure of the chimera of the C-terminal tail peptide of APP and the C-terminal PID domain of Fe65L | ||||||
![]() | Amyloid beta A4 protein and Amyloid beta A4 precursor protein-binding family B member 2 | ||||||
![]() | PROTEIN 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 | ![]() negative regulation of cell cycle phase transition / regulation of response to calcium ion / Formyl peptide receptors bind formyl peptides and many other ligands / growth cone lamellipodium / Advanced glycosylation endproduct receptor signaling / cellular response to norepinephrine stimulus / growth cone filopodium / ECM proteoglycans / maintenance of lens transparency / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane ...negative regulation of cell cycle phase transition / regulation of response to calcium ion / Formyl peptide receptors bind formyl peptides and many other ligands / growth cone lamellipodium / Advanced glycosylation endproduct receptor signaling / cellular response to norepinephrine stimulus / growth cone filopodium / ECM proteoglycans / maintenance of lens transparency / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / 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 / G alpha (q) signalling events / TAK1-dependent IKK and NF-kappa-B activation / G alpha (i) signalling events / response to yeast / Platelet degranulation / peptidase activator activity / growth factor receptor binding / Mitochondrial protein degradation / antifungal humoral response / astrocyte projection / ion binding / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / ciliary rootlet / PTB domain binding / main axon / Golgi-associated vesicle / positive regulation of amyloid fibril formation / neuron remodeling / suckling behavior / nuclear envelope lumen / dendrite development / COPII-coated ER to Golgi transport vesicle / presynaptic active zone / neuronal dense core vesicle / modulation of excitatory postsynaptic potential / neuromuscular process controlling balance / regulation of presynapse assembly / transition metal ion binding / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / intracellular copper ion homeostasis / negative regulation of neuron differentiation / smooth muscle contraction / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / positive regulation of calcium-mediated signaling / positive regulation of chemokine production / clathrin-coated pit / regulation of peptidyl-tyrosine phosphorylation / forebrain development / Notch signaling pathway / neuron projection maintenance / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / cholesterol metabolic process / positive regulation of mitotic cell cycle / response to interleukin-1 / adult locomotory behavior / extracellular matrix organization / axonogenesis / positive regulation of peptidyl-threonine phosphorylation / dendritic shaft / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / locomotory behavior / central nervous system development / long-term synaptic potentiation / positive regulation of JNK cascade / axon guidance / regulation of long-term neuronal synaptic plasticity / microglial cell activation / neuron migration / visual learning / serine-type endopeptidase inhibitor activity / neuromuscular junction / neuron differentiation / recycling endosome / memory / cognition / neuron cellular homeostasis / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
![]() | Li, H. / Koshiba, S. / Tochio, N. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() 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 |
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Remark 650 | HELIX Determination method: Author determined | ||||||
Remark 700 | SHEET Determination method: Author determined |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1001.7 KB | Display | ![]() |
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PDB format | ![]() | 845.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 343.5 KB | Display | ![]() |
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Full document | ![]() | 489.9 KB | Display | |
Data in XML | ![]() | 71.6 KB | Display | |
Data in CIF | ![]() | 88 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wguC ![]() 2rozC ![]() 2yszC ![]() 2yt1C C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 19165.221 Da / Num. of mol.: 1 / Fragment: APP peptide and PID domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 1.04mM 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 |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz |
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Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |