+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1650 | |||||||||
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Title | Reconstruction of a 13 nm wide Abeta(1-40) amyloid fibril | |||||||||
Map data | This is a reconstruction of an Abeta(1-40) amyloid fibril | |||||||||
Sample |
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Keywords | Alzheimer's disease / amyloid / prion / protein folding | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 23.0 Å | |||||||||
Authors | Schmidt M / Sachse C / Richter W / Xu C / Fandrich M / Grigorieff N | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2009 Title: Comparison of Alzheimer Abeta(1-40) and Abeta(1-42) amyloid fibrils reveals similar protofilament structures. Authors: Matthias Schmidt / Carsten Sachse / Walter Richter / Chen Xu / Marcus Fändrich / Nikolaus Grigorieff / Abstract: We performed mass-per-length (MPL) measurements and electron cryomicroscopy (cryo-EM) with 3D reconstruction on an Abeta(1-42) amyloid fibril morphology formed under physiological pH conditions. The ...We performed mass-per-length (MPL) measurements and electron cryomicroscopy (cryo-EM) with 3D reconstruction on an Abeta(1-42) amyloid fibril morphology formed under physiological pH conditions. The data show that the examined Abeta(1-42) fibril morphology has only one protofilament, although two protofilaments were observed with a previously studied Abeta(1-40) fibril. The latter fibril was resolved at 8 A resolution showing pairs of beta-sheets at the cores of the two protofilaments making up a fibril. Detailed comparison of the Abeta(1-42) and Abeta(1-40) fibril structures reveals that they share an axial twofold symmetry and a similar protofilament structure. Furthermore, the MPL data indicate that the protofilaments of the examined Abeta(1-40) and Abeta(1-42) fibrils have the same number of Abeta molecules per cross-beta repeat. Based on this data and the previously studied Abeta(1-40) fibril structure, we describe a model for the arrangement of peptides within the Abeta(1-42) fibril. | |||||||||
History |
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-Structure visualization
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1650.map.gz | 58.5 KB | EMDB map data format | |
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Header (meta data) | emd-1650-v30.xml emd-1650.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
Images | EMD-1650.tif | 37.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1650 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1650 | HTTPS FTP |
-Validation report
Summary document | emd_1650_validation.pdf.gz | 176 KB | Display | EMDB validaton report |
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Full document | emd_1650_full_validation.pdf.gz | 175.2 KB | Display | |
Data in XML | emd_1650_validation.xml.gz | 4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1650 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1650 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1650.map.gz / Format: CCP4 / Size: 62.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | This is a reconstruction of an Abeta(1-40) amyloid fibril | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.8 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Abeta(1-40) amyloid fibril
Entire | Name: Abeta(1-40) amyloid fibril |
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Components |
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-Supramolecule #1000: Abeta(1-40) amyloid fibril
Supramolecule | Name: Abeta(1-40) amyloid fibril / type: sample / ID: 1000 / Oligomeric state: Cross-beta structure / Number unique components: 1 |
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-Macromolecule #1: Abeta(1-40) peptide
Macromolecule | Name: Abeta(1-40) peptide / type: protein_or_peptide / ID: 1 / Name.synonym: Alzheimer peptide / Oligomeric state: Cross-beta / Recombinant expression: Yes / Database: NCBI |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 4.33 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8.7 / Details: 50 mM sodium borate |
Grid | Details: 400 mesh copper grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 30 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: Manual plunger (Brandeis) Method: One-sided blotting for 5 seconds before plunging |
Details | Incubation for 4 days at 4 degC |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Min: 90 K / Max: 90 K / Average: 90 K |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 4 / Average electron dose: 35 e/Å2 / Od range: 1.2 / Bits/pixel: 12 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 58090 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Details | Fibrils were selected using BOXER |
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Final reconstruction | Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Details: Final map was calculated from 4 fibrils |
CTF correction | Details: Each particle |