|Entry||Database: EMDB / ID: 1650|
|Title||Reconstruction of a 13 nm wide Abeta(1-40) amyloid fibril|
|Keywords||Alzheimer's disease / amyloid / prion / protein folding|
|Sample||Abeta(1-40) amyloid fibril|
|Source||Homo sapiens / human|
|Map data||This is a reconstruction of an Abeta(1-40) amyloid fibril|
|Method||helical reconstruction, at 23 Å resolution|
|Authors||Schmidt M / Sachse C / Richter W / Xu C / Fandrich M / Grigorieff N|
|Citation||Proc. Natl. Acad. Sci. U.S.A., 2009, 106, 19813-19818|
Proc. Natl. Acad. Sci. U.S.A., 2009, 106, 19813-19818 Yorodumi Papers
|Date||Deposition: Sep 11, 2009 / Header (metadata) release: Sep 24, 2009 / Map release: Sep 24, 2009 / Last update: Apr 13, 2016|
Downloads & links
|File||emd_1650.map.gz (map file in CCP4 format, 64 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 4.8 Å|
CCP4 map header:
-Entire Abeta(1-40) amyloid fibril
|Entire||Name: Abeta(1-40) amyloid fibril / Number of components: 1 / Oligomeric State: Cross-beta structure|
-Component #1: protein, Abeta(1-40) peptide
|Protein||Name: Abeta(1-40) peptide / a.k.a: Alzheimer peptide / Oligomeric Details: Cross-beta / Recombinant expression: Yes|
|Mass||Theoretical: 4.33 kDa|
|Source||Species: Homo sapiens / human|
|Specimen state||helical array|
|Helical parameters||Axial symmetry: C2 (2 fold cyclic) / Hand: LEFT HANDED|
|Crystal grow details||Incubation for 4 days at 4 degC|
|Sample solution||Specimen conc.: 1 mg/ml / Buffer solution: 50 mM sodium borate / pH: 8.7|
|Support film||400 mesh copper grid|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 30 % / Method: One-sided blotting for 5 seconds before plunging|
Details: Vitrification instrument: Manual plunger (Brandeis)
-Electron microscopy imaging
Model: Tecnai F30 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F30|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 35 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 59000 X (nominal), 58090 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 3500 nm|
|Specimen Holder||Holder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 90 K ( 90 - 90 K)|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 4 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 12 / OD range: 1.2|
|Processing||Method: helical reconstruction / Details: Fibrils were selected using BOXER|
|3D reconstruction||Algorithm: Weighted back projection / Software: Spider / CTF correction: Each particle / Details: Final map was calculated from 4 fibrils / Resolution: 23 Å / Resolution method: FSC 0.5|
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