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- EMDB-70523: Structure of Type II ABri amyloid filaments extracted from human ... -

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Basic information

Entry
Database: EMDB / ID: EMD-70523
TitleStructure of Type II ABri amyloid filaments extracted from human brain of Familial British Dementia patient
Map data
Sample
  • Tissue: ABri amyloid filament
    • Protein or peptide: ABri (ITM2B mutant)
    • RNA: unknown protein
Keywordsamyloid / filament / neurodegeneration / brain / ex vivo / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsOzcan KA / Vago F / Bharath SR / Jiang W / Vidal R
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA) United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: To Be Published
Title: Cryo-EM structures of ADan and ABri filaments from FDD and FBD
Authors: Ozcan KA / Vago F / Bharath SR / Jiang W / Vidal R
History
DepositionMay 6, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70523.png

Downloads & links

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Map

FileDownload / File: emd_70523.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 300 pix.
= 246.6 Å		0.82 Å/pix.
x 300 pix.
= 246.6 Å		0.82 Å/pix.
x 300 pix.
= 246.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00876
Minimum - Maximum-0.02584081 - 0.04902523
Average (Standard dev.)0.0000481261 (±0.0010113835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 246.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_70523_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70523_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70523_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ABri amyloid filament

EntireName: ABri amyloid filament
Components
  • Tissue: ABri amyloid filament
    • Protein or peptide: ABri (ITM2B mutant)
    • RNA: unknown protein

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Supramolecule #1: ABri amyloid filament

SupramoleculeName: ABri amyloid filament / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: ABri (ITM2B mutant)

MacromoleculeName: ABri (ITM2B mutant) / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.676227 KDa
SequenceString:
ASNCFAIRHF ENKFAVETLI CSRTVKKNIA EE

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Macromolecule #2: unknown protein

MacromoleculeName: unknown protein / type: rna / ID: 2 / Number of copies: 5
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 550.776 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.77 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.08 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24596
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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