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- EMDB-58700: Amyloid beta oligomer Interactions with Extracellular Vesicles by... -

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Basic information

Entry
Database: EMDB / ID: EMD-58700
TitleAmyloid beta oligomer Interactions with Extracellular Vesicles by Cryo-ET
Map dataSmall extracellular vesicle with Amyloid beta oligomers 42
Sample
  • Organelle or cellular component: Small extracellular vesicles with Amyloid beta oligomers
KeywordsAmyloid beta / Small extracellular vesicles / cryo-electron tomography / LIPID BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM / Resolution: 6.7 Å
AuthorsKhursheed A / Viles JH / Zhang H / Shang Q / Tian Y / Szwedziak P / Volkov VA
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/Y001931/1 United Kingdom
CitationJournal: To Be Published
Title: Amyloid beta oligomer Interactions with Extracellular Vesicles by Cryo-ET
Authors: Khursheed A / Viles JH / Zhang H / Shang Q / Tian Y / Szwedziak P / Volkov VA
History
DepositionJun 26, 2026-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58700.png

Downloads & links

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Map

FileReleased
AnnotationSmall extracellular vesicle with Amyloid beta oligomers 42
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
67 Å/pix.
x 318 pix.
= 21306. Å		67 Å/pix.
x 1440 pix.
= 96480. Å		67 Å/pix.
x 1024 pix.
= 68608. Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 67 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.2216688 - 0.37345695
Average (Standard dev.)-0.0022366177 (±0.0028788995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions14401024318
Spacing10241440318
CellA: 68608.0 Å / B: 96480.0 Å / C: 21306.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Small extracellular vesicles with Amyloid beta oligomers

EntireName: Small extracellular vesicles with Amyloid beta oligomers
Components
  • Organelle or cellular component: Small extracellular vesicles with Amyloid beta oligomers

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Supramolecule #1: Small extracellular vesicles with Amyloid beta oligomers

SupramoleculeName: Small extracellular vesicles with Amyloid beta oligomers
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Details: Small extracellular vesicles with Amyloid beta oligomers
Source (natural)Organism: Homo sapiens (human) / Strain: HEK 293 cell / Organelle: small extracellular vesicles

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Component - Concentration: 30.0 mM / Component - Formula: HEPES
Component - Name: 2-hydroxyethyl)-1-piperazineethanesulfonic acid
Details: Sodium phosphate buffer 30 mM and phosphate-buffered saline
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 277.15 K / Instrument: LEICA EM GP
Detailssmall extracellular vesicles incubated with amyloid beta oligomers
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Ted Pella / Diameter: 5 nm

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 0.4 sec. / Average electron dose: 2.92 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 53000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Software - Name: IMOD / Number images used: 41
CTF correctionType: NONE

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