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Yorodumi- EMDB-5132: The reconstructed F120 amyloid fibril represents the structure of... -
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-Basic information
Entry | Database: EMDB / ID: EMD-5132 | |||||||||
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Title | The reconstructed F120 amyloid fibril represents the structure of a selected subpopulation from the Abeta(1-40) fibril sample with a mean crossover distance of 120 nm. The F140 subpopulation with a mean crossover distance of 140 nm had been studied and deposited previously (EMDB accession no. 5008). | |||||||||
Map data | Cross-sectional density slice of the F120 amyloid fibril of 24 Angstrom thickness. F120 corresponds to a subpopulation of the Abeta(1-40) amyloid fibril sample with a mean crossover distance of 120 nm. | |||||||||
Sample |
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Keywords | Alzheimer's disease / micromechanical properties / electron cryo-microscopy / amyloid fibrils | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / negative staining / Resolution: 10.1 Å | |||||||||
Authors | Sachse C / Faendrich M / Grigorieff N | |||||||||
Citation | Journal: Angew Chem Int Ed Engl / Year: 2010 Title: Nanoscale flexibility parameters of Alzheimer amyloid fibrils determined by electron cryo-microscopy. Authors: Carsten Sachse / Nikolaus Grigorieff / Marcus Fändrich / | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5132.map.gz | 285.4 KB | EMDB map data format | |
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Header (meta data) | emd-5132-v30.xml emd-5132.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
Images | emd_5132_1.tif | 54.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5132 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5132 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5132.map.gz / Format: CCP4 / Size: 306.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cross-sectional density slice of the F120 amyloid fibril of 24 Angstrom thickness. F120 corresponds to a subpopulation of the Abeta(1-40) amyloid fibril sample with a mean crossover distance of 120 nm. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Human Abeta (1-40)
Entire | Name: Human Abeta (1-40) |
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Components |
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-Supramolecule #1000: Human Abeta (1-40)
Supramolecule | Name: Human Abeta (1-40) / type: sample / ID: 1000 / Oligomeric state: helical / Number unique components: 1 |
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Molecular weight | Theoretical: 4.33 KDa |
-Macromolecule #1: Abeta
Macromolecule | Name: Abeta / type: protein_or_peptide / ID: 1 / Name.synonym: Abeta / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8.7 / Details: 50 mM Borate |
Staining | Type: NEGATIVE / Details: Blot for 7 seconds before plunging |
Grid | Details: Quantifoil 400 mesh 1.3 micrometer holes |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 77.2 K / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: custom-built plunging apparatus. in coldroom at 277 K. Method: Blot for 7 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Average: 93 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 200,000 times magnification |
Date | Nov 9, 2005 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 62 / Average electron dose: 35 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 58333 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.9 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Details | The fibrils in the sample were selected based on their uniform width. 2. The F120 subset of limited crossover distances (110-130 nm) was chosen for the reconstruction. |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 4.8 Å Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.1 Å / Resolution method: OTHER / Software - Name: SPIDER |
CTF correction | Details: Each particle CTFTILT |
Final angle assignment | Details: one-degree sampling around helical axis, out-of-plane tilt 16 degree deviation (in 1 degree steps) |