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Yorodumi- EMDB-6327: 3D reconstruction from the 188 most curved out of 450 fibrils of ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6327 | |||||||||
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Title | 3D reconstruction from the 188 most curved out of 450 fibrils of Abeta(1-40) | |||||||||
Map data | 3D reconstruction of Abeta(1-40) fibril before any filtering, symmetrization, or masking. Figure 5A of the primary citation was generated from this map by application of helical symmetry and a B factor of -600A^2, with low-pass filtering to 7.5A. | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 8.3 Å | |||||||||
Authors | Rohou A / Grigorieff N | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2008 Title: Paired beta-sheet structure of an Abeta(1-40) amyloid fibril revealed by electron microscopy. Authors: Carsten Sachse / Marcus Fändrich / Nikolaus Grigorieff / Abstract: Alzheimer's disease is a neurodegenerative disorder that is characterized by the cerebral deposition of amyloid fibrils formed by Abeta peptide. Despite their prevalence in Alzheimer's and other ...Alzheimer's disease is a neurodegenerative disorder that is characterized by the cerebral deposition of amyloid fibrils formed by Abeta peptide. Despite their prevalence in Alzheimer's and other neurodegenerative diseases, important details of the structure of amyloid fibrils remain unknown. Here, we present a three-dimensional structure of a mature amyloid fibril formed by Abeta(1-40) peptide, determined by electron cryomicroscopy at approximately 8-A resolution. The fibril consists of two protofilaments, each containing approximately 5-nm-long regions of beta-sheet structure. A local twofold symmetry within each region suggests that pairs of beta-sheets are formed from equivalent parts of two Abeta(1-40) peptides contained in each protofilament. The pairing occurs via tightly packed interfaces, reminiscent of recently reported steric zipper structures. However, unlike these previous structures, the beta-sheet pairing is observed within an amyloid fibril and includes significantly longer amino acid sequences. | |||||||||
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_6327.map.gz | 365.1 MB | EMDB map data format | |
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Header (meta data) | emd-6327-v30.xml emd-6327.xml | 10 KB 10 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6327_fsc.xml | 21.1 KB | Display | FSC data file |
Images | emd_6327.jpg | 10.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6327 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6327 | HTTPS FTP |
-Validation report
Summary document | emd_6327_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_6327_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_6327_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6327 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6327 | 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_6327.map.gz / Format: CCP4 / Size: 494.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D reconstruction of Abeta(1-40) fibril before any filtering, symmetrization, or masking. Figure 5A of the primary citation was generated from this map by application of helical symmetry and a B factor of -600A^2, with low-pass filtering to 7.5A. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2 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 assembly / Number unique components: 1 |
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-Macromolecule #1: Amyloid beta peptide (1-40)
Macromolecule | Name: Amyloid beta peptide (1-40) / type: protein_or_peptide / ID: 1 / Name.synonym: Abeta(1-40) / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Homo sapiens (human) / synonym: human |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.8 / Details: 50 mM borate |
Grid | Details: Quantifoil R1.2/1.3 Cu 400 mesh grids |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification carried out in cold room at 277 K. / Method: Blot for 7 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Date | Feb 9, 2006 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7.0 µm / Number real images: 63 / Average electron dose: 35 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.629 µm / Nominal defocus min: 2.027 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |