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Yorodumi- PDB-6w0o: Amyloid-beta(1-40) fibril derived from Alzheimer's disease cortic... -
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-Basic information
Entry | Database: PDB / ID: 6w0o | ||||||
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Title | Amyloid-beta(1-40) fibril derived from Alzheimer's disease cortical tissue | ||||||
Components | Amyloid-beta precursor protein | ||||||
Keywords | PROTEIN FIBRIL / amyloid-beta / Alzheimer's disease | ||||||
Function / homology | Function and homology information regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of Wnt signaling pathway / regulation of synapse structure or activity / 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 Wnt signaling pathway / regulation of synapse structure or activity / 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 / negative regulation of neuron differentiation / intracellular copper ion homeostasis / 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 / response to interleukin-1 / positive regulation of mitotic cell cycle / adult locomotory behavior / axonogenesis / extracellular matrix organization / positive regulation of peptidyl-threonine phosphorylation / platelet alpha granule lumen / trans-Golgi network membrane / dendritic shaft / learning / positive regulation of interleukin-1 beta production / locomotory behavior / positive regulation of long-term synaptic potentiation / central nervous system development / endosome lumen / astrocyte activation / positive regulation of JNK cascade / Post-translational protein phosphorylation / synapse organization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / 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 / positive regulation of interleukin-6 production / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of tumor necrosis factor production / neuron projection development / cell-cell junction / synaptic vesicle Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / SOLID-STATE NMR / helical reconstruction / simulated annealing / cryo EM / Resolution: 2.77 Å | ||||||
Authors | Ghosh, U. / Thurber, K.R. / Tycko, R. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Molecular structure of a prevalent amyloid-β fibril polymorph from Alzheimer's disease brain tissue. Authors: Ujjayini Ghosh / Kent R Thurber / Wai-Ming Yau / Robert Tycko / Abstract: Amyloid-β (Aβ) fibrils exhibit self-propagating, molecular-level polymorphisms that may contribute to variations in clinical and pathological characteristics of Alzheimer's disease (AD). We report ...Amyloid-β (Aβ) fibrils exhibit self-propagating, molecular-level polymorphisms that may contribute to variations in clinical and pathological characteristics of Alzheimer's disease (AD). We report the molecular structure of a specific fibril polymorph, formed by 40-residue Aβ peptides (Aβ40), that is derived from cortical tissue of an AD patient by seeded fibril growth. The structure is determined from cryogenic electron microscopy (cryoEM) images, supplemented by mass-per-length (MPL) measurements and solid-state NMR (ssNMR) data. Previous ssNMR studies with multiple AD patients had identified this polymorph as the most prevalent brain-derived Aβ40 fibril polymorph from typical AD patients. The structure, which has 2.8-Å resolution according to standard criteria, differs qualitatively from all previously described Aβ fibril structures, both in its molecular conformations and its organization of cross-β subunits. Unique features include twofold screw symmetry about the fibril growth axis, despite an MPL value that indicates three Aβ40 molecules per 4.8-Å β-sheet spacing, a four-layered architecture, and fully extended conformations for molecules in the central two cross-β layers. The cryoEM density, ssNMR data, and MPL data are consistent with β-hairpin conformations for molecules in the outer cross-β layers. Knowledge of this brain-derived fibril structure may contribute to the development of structure-specific amyloid imaging agents and aggregation inhibitors with greater diagnostic and therapeutic utility. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6w0o.cif.gz | 549.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w0o.ent.gz | 462.2 KB | Display | PDB format |
PDBx/mmJSON format | 6w0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w0o_validation.pdf.gz | 418.2 KB | Display | wwPDB validaton report |
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Full document | 6w0o_full_validation.pdf.gz | 609.3 KB | Display | |
Data in XML | 6w0o_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 6w0o_validation.cif.gz | 42 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/6w0o ftp://data.pdbj.org/pub/pdb/validation_reports/w0/6w0o | HTTPS FTP |
-Related structure data
Related structure data | 21501MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 6 / Rise per n subunits: 2.45 Å / Rotation per n subunits: 179.66 °) |
-Components
#1: Protein/peptide | Mass: 4335.852 Da / Num. of mol.: 6 / Fragment: UNP residues 653-692 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067 |
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-Experimental details
-Experiment
Experiment |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction | ||||||||||||||||||||||||||||||||||||
NMR experiment |
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-Sample preparation
Component | Name: amyloid-beta(1-40) fibrils derived from human AD brain Type: COMPLEX Details: Fibrils produced by seeded growth using amyloid-beta in brain extract as the source of seeds. CryoEM and solid state NMR measurements were performed on second-generation seeded fibrils. Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 29 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 Details: 10 mM phosphate buffer with 0.01% NaN3 to avoid microbial contamination. Buffers were filtered to avoid contamination. |
Buffer component | Conc.: 10 mM / Name: Phosphate buffer / Formula: Na2HPO4/NaH2PO4 |
Specimen | Conc.: 0.45 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Protein exists in solution as amyloid fibrils of varying lengths. |
Specimen support | Details: The grids were checked in microscope prior to use. / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: LEICA PLUNGER / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K Details: The grids were preblotted for 10 seconds and blotted for 6 seconds before plunging. |
Details | Type: fibrous protein Contents: 100 uM U-15N,13C amyloid-beta(1-40), phosphate buffer Details: lyophilized, rehydrated in MAS rotor, 100 uM concentration prior to pelleting Label: U-labeled fibrils / Solvent system: phosphate buffer |
Sample | Conc.: 100 uM / Component: amyloid-beta(1-40) / Isotopic labeling: U-15N,13C |
Sample conditions | Details: pelleted, lyophilized, rehydrated in MAS rotor / Ionic strength: 10 mM / Label: conditions_1 / pH: 7.4 / PH err: 0.05 / Pressure: 1 atm / Temperature: 297 K / Temperature err: 2 |
-Data collection
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS Details: Preliminary grid screening was done manually in FEI T12. |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: -3000 nm / Nominal defocus min: -500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Residual tilt: 6 mradians |
Image recording | Average exposure time: 10 sec. / Electron dose: 73.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1337 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 50 / Used frames/image: 1-50 |
NMR spectrometer | Type: Varian InfinityPlus / Manufacturer: Varian / Model: InfinityPlus / Field strength: 600 MHz |
-Processing
EM software |
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Image processing | Details: The selected images were corrected for gain. The gain reference was not rotated or flipped. | ||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: The correction was done in Gctf and is corrected for amplitude. Per -particle CTF refinement was done prior to final reconstruction. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 179.66 ° / Axial rise/subunit: 2.45 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 19790 Details: The particles were picked using Relion manual pick, with a 20A low pass filter and particle diameter of 30A. | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14775 / Algorithm: FOURIER SPACE Details: A modified version of RELION 3.0-beta was used for the reconstruction. The modified version allowed local averaging of the rotation angle. Final reconstruction used 2-fold screw symmetry. Num. of class averages: 1 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL Details: Xplor-NIH was used to combine EM density with phi/psi restraints from NMR chemical shifts (from Talos-N Version 4.21 Rev 2016.343.11.31). | ||||||||||||||||||||||||||||||||||||||||||||||||||
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 3 Details: phi/psi from TalosN & EM density used as restraints | ||||||||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 60 / Conformers submitted total number: 10 |