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Yorodumi- PDB-3ktm: Structure of the Heparin-induced E1-Dimer of the Amyloid Precurso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ktm | ||||||
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Title | Structure of the Heparin-induced E1-Dimer of the Amyloid Precursor Protein (APP) | ||||||
Components | Amyloid beta A4 protein | ||||||
Keywords | CELL ADHESION / SIGNALING PROTEIN / Protein Structure / Alzheimer disease / Amyloid / Amyloidosis / Apoptosis / Copper / Disease mutation / Disulfide bond / Endocytosis / Heparin-binding / Metal-binding / Neurodegeneration / Notch signaling pathway / Proteoglycan / Zinc | ||||||
Function / homology | Function and homology information regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis ...regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / regulation of Wnt signaling pathway / mating behavior / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / positive regulation of amyloid fibril formation / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / : / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / presynaptic active zone / nuclear envelope lumen / modulation of excitatory postsynaptic potential / suckling behavior / COPII-coated ER to Golgi transport vesicle / dendrite development / smooth endoplasmic reticulum / regulation of NMDA receptor activity / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / regulation of presynapse assembly / The NLRP3 inflammasome / intracellular copper ion homeostasis / transition metal ion binding / regulation of multicellular organism growth / negative regulation of long-term synaptic potentiation / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / forebrain development / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / positive regulation of G2/M transition of mitotic cell cycle / ionotropic glutamate receptor signaling pathway / positive regulation of protein metabolic process / neuron projection maintenance / cholesterol metabolic process / extracellular matrix organization / positive regulation of glycolytic process / positive regulation of mitotic cell cycle / response to interleukin-1 / axonogenesis / adult locomotory behavior / trans-Golgi network membrane / dendritic shaft / locomotory behavior / platelet alpha granule lumen / positive regulation of peptidyl-threonine phosphorylation / learning / central nervous system development / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / astrocyte activation / endosome lumen / synapse organization / Post-translational protein phosphorylation / regulation of long-term neuronal synaptic plasticity / positive regulation of JNK cascade / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / visual learning / neuromuscular junction / serine-type endopeptidase inhibitor activity / recycling endosome / cognition / positive regulation of inflammatory response / Golgi lumen / neuron cellular homeostasis / endocytosis / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to amyloid-beta / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / positive regulation of DNA-binding transcription factor activity / G2/M transition of mitotic cell cycle / cell-cell junction / synaptic vesicle / positive regulation of tumor necrosis factor production / regulation of translation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Dahms, S.O. / Hoefgen, S. / Roeser, D. / Schlott, B. / Guhrs, K.H. / Than, M.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structure and biochemical analysis of the heparin-induced E1 dimer of the amyloid precursor protein. Authors: Dahms, S.O. / Hoefgen, S. / Roeser, D. / Schlott, B. / Guhrs, K.H. / Than, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ktm.cif.gz | 292.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ktm.ent.gz | 237.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ktm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/3ktm ftp://data.pdbj.org/pub/pdb/validation_reports/kt/3ktm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
-Components
#1: Protein | Mass: 21762.080 Da / Num. of mol.: 8 / Fragment: UNP residues 18-190 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APP, A4, AD1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: P05067 #2: Chemical | ChemComp-BU4 / ( #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-ACT / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 19, 2008 Details: Double crystal monochromator with 2 sets of mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→29 Å / Num. obs: 74422 / % possible obs: 99.8 % / Redundancy: 2.1 % / Biso Wilson estimate: 69.152 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.7→2.85 Å / % possible obs: 99.7 % / Redundancy: 2 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.1 / Num. unique all: 10822 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MWP, 2FJZ Resolution: 2.7→29 Å
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Displacement parameters | Biso mean: 48.6 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→29 Å
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Refine LS restraints |
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