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Yorodumi- 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 | ||||||
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Title | Solution structure of the chimera of the C-terminal PID domain of Fe65L and the C-terminal tail peptide of APP | ||||||
Components | Amyloid beta A4 precursor protein-binding family B member 2 and Amyloid beta A4 protein | ||||||
Keywords | 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 | Function and homology information 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 / cellular response to norepinephrine stimulus / Advanced glycosylation endproduct receptor signaling / 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 / cellular response to norepinephrine stimulus / Advanced glycosylation endproduct receptor signaling / 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 / peptidase activator activity / Platelet degranulation / growth factor receptor binding / antifungal humoral response / astrocyte projection / Mitochondrial protein degradation / 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 / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / ciliary rootlet / PTB domain binding / Golgi-associated vesicle / main axon / positive regulation of amyloid fibril formation / neuron remodeling / nuclear envelope lumen / suckling behavior / COPII-coated ER to Golgi transport vesicle / dendrite development / neuronal dense core vesicle / presynaptic active zone / modulation of excitatory postsynaptic potential / neuromuscular process controlling balance / negative regulation of long-term synaptic potentiation / regulation of presynapse assembly / transition metal ion binding / regulation of multicellular organism growth / negative regulation of neuron differentiation / intracellular copper ion homeostasis / smooth muscle contraction / spindle midzone / positive regulation of T cell migration / smooth endoplasmic reticulum / regulation of peptidyl-tyrosine phosphorylation / clathrin-coated pit / positive regulation of chemokine production / forebrain development / Notch signaling pathway / neuron projection maintenance / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / positive regulation of calcium-mediated signaling / ionotropic glutamate receptor signaling pathway / cholesterol metabolic process / positive regulation of glycolytic process / extracellular matrix organization / positive regulation of mitotic cell cycle / response to interleukin-1 / axonogenesis / adult locomotory behavior / positive regulation of peptidyl-threonine phosphorylation / dendritic shaft / positive regulation of interleukin-1 beta production / axon guidance / positive regulation of long-term synaptic potentiation / central nervous system development / locomotory behavior / long-term synaptic potentiation / positive regulation of JNK cascade / neuron migration / microglial cell activation / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / visual learning / neuromuscular junction / recycling endosome / neuron differentiation / memory / cognition / positive regulation of inflammatory response / positive regulation of interleukin-6 production / neuron cellular homeostasis / positive regulation of non-canonical NF-kappaB signal transduction Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Li, H. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: 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 |
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Remark 650 | HELIX Determination method: Author determined | ||||||
Remark 700 | SHEET Determination method: Author determined |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ysz.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2ysz.ent.gz | 882.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ysz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ysz_validation.pdf.gz | 346 KB | Display | wwPDB validaton report |
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Full document | 2ysz_full_validation.pdf.gz | 513.5 KB | Display | |
Data in XML | 2ysz_validation.xml.gz | 75.8 KB | Display | |
Data in CIF | 2ysz_validation.cif.gz | 92.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/2ysz ftp://data.pdbj.org/pub/pdb/validation_reports/ys/2ysz | HTTPS FTP |
-Related structure data
Related structure data | 1wguC 2rozC 2yt0C 2yt1C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 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 |
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Sample conditions | Ionic strength: 120mM / pH: 7 / 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 |