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- EMDB-75655: Structure of Rapidly twisting Amyloid-beta 40 fibril , RT-Ab40(C1)' -

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Basic information

Entry
Database: EMDB / ID: EMD-75655
TitleStructure of Rapidly twisting Amyloid-beta 40 fibril , RT-Ab40(C1)'
Map dataStructure of Rapidly twisting Amyloid-beta 40 fibril , RT-Ab40(C1)'
Sample
  • Complex: amyloid-b 40 fibril
    • Protein or peptide: Amyloid beta 40
KeywordsAmyloid-beta 40 / rapidly twisting / protein fibril / Ab40
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsLarimi MG / Thurber KR / Tycko R
Funding support1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)
CitationJournal: bioRxiv / Year: 2026
Title: Polymorphic structures of rapidly twisting 40-residue amyloid-β fibrils.
Authors: Motahareh G Larimi / Kent R Thurber / Robert Tycko /
Abstract: Fibrils formed by 40- and 42-residue amyloid-β peptides (Aβ40 and Aβ42) are polymorphic, containing molecular structures that vary with growth conditions in ways that are not fully understood. ...Fibrils formed by 40- and 42-residue amyloid-β peptides (Aβ40 and Aβ42) are polymorphic, containing molecular structures that vary with growth conditions in ways that are not fully understood. Here we use cryogenic electron microscopy to characterize the structure of rapidly twisting Aβ40 fibrils, for which the distance between apparent width minima in electron microscope images ("cross-over distances") is approximately 25 nm. From samples grown under a single set of growth conditions, we obtain high-resolution structures for three different rapidly twisting polymorphs. Although their cross-over distances are similar, the three rapidly twisting polymorphs differ in twist handedness, symmetry, molecular conformations, and intermolecular contacts. Two of the rapidly twisting polymorphs resemble slowly twisting Aβ40 polymorphs that have been described previously, including polymorphs extracted from brain tissue of Alzheimer's disease patients or created by seeded growth from amyloid in brain tissue, but with shorter conformationally ordered segments and other specific conformational differences. These results contribute to our understanding of amyloid polymorphism, connections between morphology and molecular structure, and relationships between brain-derived and -grown fibrils.
History
DepositionFeb 19, 2026-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75655.png

Downloads & links

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Map

FileDownload / File: emd_75655.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of Rapidly twisting Amyloid-beta 40 fibril , RT-Ab40(C1)'
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 500 pix.
= 410. Å		0.82 Å/pix.
x 500 pix.
= 410. Å		0.82 Å/pix.
x 500 pix.
= 410. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0069
Minimum - Maximum-0.015008678 - 0.03079303
Average (Standard dev.)0.000033440356 (±0.00049695466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 410.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Additional Map

Fileemd_75655_additional_1.map
AnnotationAdditional Map
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Half map: Half Map A

Fileemd_75655_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_75655_half_map_2.map
AnnotationHalf Map B
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Sample components

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Entire : amyloid-b 40 fibril

EntireName: amyloid-b 40 fibril
Components
  • Complex: amyloid-b 40 fibril
    • Protein or peptide: Amyloid beta 40

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Supramolecule #1: amyloid-b 40 fibril

SupramoleculeName: amyloid-b 40 fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Amyloid beta 40

MacromoleculeName: Amyloid beta 40 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV

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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: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.28 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.76 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.96 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 22361
Startup modelType of model: NONE
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Residue range: 13-40 / Chain - Source name: Other / Chain - Initial model type: other / Details: built manually in coot
RefinementSpace: REAL / Protocol: AB INITIO MODEL

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