Additional file 2 of Cryo-EM structures of Aβ40 filaments from the leptomeninges of individuals with Alzheimer’s disease and cerebral amyloid angiopathy
Creators: name: Yang, Yang
name: Murzin, Alexey G.
name: Peak-Chew, Sew
name: Franco, Catarina
name: Garringer, Holly J.
name: Newell, Kathy L.
name: Ghetti, Bernardino
name: Goedert, Michel
name: Scheres, Sjors H. W.
Publisher: name: figshare
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Cell Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Chemical Sciences not elsewhere classified

description: Additional file 2: Fig. S1. Cryo-EM micrographs and processing details. a Cryo-EM micrographs of Aβ40 filaments from the leptomeninges of case 1 following sarkosyl extraction. The orange arrowhead points to a type 1 filament, whereas the cyan arrowhead points to a type 2 filament. Scale bar, 50 nm. b, c Two-dimensional class average plots of type 1 (b) and type 2 (c) Aβ40 filaments from the leptomeninges of case 1 following sarkosyl extraction. Scale bar, 5 nm. d, e Three-dimensional reconstructions of type 1 (d) and type 2 (e) Aβ40 filaments from the leptomeninges of case 1 following sarkosyl extraction. Scale bar, 2 nm. f, g Fourier shell correlation (FSC) curves for the cryo-EM maps of type 1 filaments (f) and type 2 filaments (g) are shown in black; for the refined atomic model against the cryo-EM map in red; for the atomic model refined in the first half map against that half map in blue; for the refined atomic model in the first half map against the other half map in yellow. Fig. S2. Summary of cryo-EM dataset of case 1 following sarkosyl extraction. a Hierarchical classification of individual filament segments according to their assigned two-dimensional class averages (vertical) and the picked filaments (horizontal). The segment clusters are labelled with Roman numbers. b Two-dimensional class averages of solved Aβ40 filaments. Cluster number and filament type are indicated above each panel. c Two-dimensional class averages of unsolved filaments. Cluster number and filament type are indicated above each panel. Fig. S3. Summary of cryo-EM dataset of case 1 following aqueous extraction. a Hierarchical classification of individual filament segments according to their assigned two-dimensional class averages (vertical) and the picked filaments (horizontal). The segment clusters are labelled with Roman numbers. b Two-dimensional class averages of solved Aβ40 filaments. Cluster number and filament type are indicated above each panel. c Two-dimensional class averages of unsolved filaments. The cluster number and filament type are indicated above each panel. Fig. S4. Summary of cryo-EM dataset of case 2 following sarkosyl extraction. a Hierarchical classification of individual filament segments according to their two-dimensional class averages (vertical) and the picked filaments (horizontal). The segment clusters are labelled with Roman numbers. b Two-dimensional class averages of solved Aβ40 filaments. Cluster number and filament type are indicated above each panel. c Two-dimensional class averages of unsolved filaments. Cluster number and filament type are indicated above each panel. Fig. S5. Summary of cryo-EM dataset of case 3 following sarkosyl extraction. a Hierarchical classification of individual filament segments according to their two-dimensional class averages (vertical) and the picked filaments (horizontal). The segment clusters are labelled with Roman numbers. b Two-dimensional class averages of solved Aβ40 filaments. Cluster number and filament type are indicated above each panel. c Two-dimensional class averages of unsolved filaments. Cluster number and filament type are indicated above each panel. The question mark after “PHF” indicates that this type probably corresponded to a PHF.