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Open data
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Basic information
Entry | Database: PDB / ID: 6ti5 | ||||||
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Title | A New Structural Model of Abeta(1-40) Fibrils | ||||||
![]() | Amyloid-beta precursor protein | ||||||
![]() | PROTEIN FIBRIL / amyloid beta peptides / Alzheimer's disease / supramolecular assembly | ||||||
Function / homology | ![]() regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity ...regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / 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 / NMDA selective glutamate receptor signaling pathway / 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 / suckling behavior / nuclear envelope lumen / dendrite development / COPII-coated ER to Golgi transport vesicle / presynaptic active zone / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / The NLRP3 inflammasome / 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 / ECM proteoglycans / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / positive regulation of chemokine production / clathrin-coated pit / regulation of peptidyl-tyrosine phosphorylation / forebrain development / Notch signaling pathway / Mitochondrial protein degradation / 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 / platelet alpha granule lumen / trans-Golgi network membrane / positive regulation of peptidyl-threonine phosphorylation / dendritic shaft / learning / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / locomotory behavior / central nervous system development / endosome lumen / astrocyte activation / positive regulation of JNK cascade / Post-translational protein phosphorylation / synapse organization / regulation of long-term neuronal synaptic plasticity / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / visual learning / serine-type endopeptidase inhibitor activity / neuromuscular junction / recycling endosome / cognition / neuron cellular homeostasis / Golgi lumen / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / endocytosis / cellular response to amyloid-beta / G2/M transition of mitotic cell cycle / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / neuron projection development / cell-cell junction / synaptic vesicle Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLID-STATE NMR / molecular dynamics | ||||||
![]() | Bertini, I. / Gonnelli, L. / Luchinat, C. / Mao, J. / Nesi, A. | ||||||
![]() | ![]() Title: Mixing A beta (1-40) and A beta (1-42) peptides generates unique amyloid fibrils. Authors: Cerofolini, L. / Ravera, E. / Bologna, S. / Wiglenda, T. / Boddrich, A. / Purfurst, B. / Benilova, I. / Korsak, M. / Gallo, G. / Rizzo, D. / Gonnelli, L. / Fragai, M. / De Strooper, B. / ...Authors: Cerofolini, L. / Ravera, E. / Bologna, S. / Wiglenda, T. / Boddrich, A. / Purfurst, B. / Benilova, I. / Korsak, M. / Gallo, G. / Rizzo, D. / Gonnelli, L. / Fragai, M. / De Strooper, B. / Wanker, E.E. / Luchinat, C. #1: Journal: J. Am. Chem. Soc. / Year: 2011 Title: A new structural model of Abeta40 fibrils. Authors: Bertini, I. / Gonnelli, L. / Luchinat, C. / Mao, J. / Nesi, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 557.2 KB | Display | ![]() |
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PDB format | ![]() | 466.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 613 KB | Display | ![]() |
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Full document | ![]() | 852.6 KB | Display | |
Data in XML | ![]() | 36.1 KB | Display | |
Data in CIF | ![]() | 53.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ti6C ![]() 6ti7C C: citing same article ( |
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Similar structure data | |
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 4335.852 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLID-STATE NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Type: fiber Contents: 100 uM [U-100% 13C; U-100% 15N] Amyloid beta peptide 1-40, 50 mM ammonium acetate, H2O Details: The fibrils were grown in ammonium acetate buffer and then washed with fresh, cold ultrapure water (Millipore) three times. Label: 13C 15N Ab(1-40) / Solvent system: H2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0 Not defined / Label: condition_1 / pH: 8.5 / Pressure: 1 atm / Temperature: 283 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 4 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: Top 4 Structures From HADDOCK / Conformers calculated total number: 200 / Conformers submitted total number: 4 |