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- EMDB-43330: Tomogram of human Alzheimer's disease brain tissue showing variet... -

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Basic information

Entry
Database: EMDB / ID: EMD-43330
TitleTomogram of human Alzheimer's disease brain tissue showing variety of membrane vesicles and axonal cross-sections
Map dataTomogram of human Alzheimer's disease brain tissue
Sample
  • Tissue: human Alzheimer's disease brain tissue
Keywordsautophagy / myelin / neuron / tissue / brain / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsCreekmore BC / Lee EB / Chang Y-W
Funding support United States, 13 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-2309043 United States
Other privateDeCrane Family Fund for PPA Research
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1AG065341 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)P30AG072979 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)P01AG066597 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)U19AG062418 United States
David and Lucile Packard Foundation2019-69645 United States
Burroughs Wellcome Fund1022785 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RM1GM136511 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)F30AG077756 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)F30CA261198 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130302 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM132039 United States
CitationJournal: Nat Commun / Year: 2024
Title: Ultrastructure of human brain tissue vitrified from autopsy revealed by cryo-ET with cryo-plasma FIB milling.
Authors: Benjamin C Creekmore / Kathryn Kixmoeller / Ben E Black / Edward B Lee / Yi-Wei Chang /
Abstract: Ultrastructure of human brain tissue has traditionally been examined using electron microscopy (EM) following fixation, staining, and sectioning, which limit resolution and introduce artifacts. ...Ultrastructure of human brain tissue has traditionally been examined using electron microscopy (EM) following fixation, staining, and sectioning, which limit resolution and introduce artifacts. Alternatively, cryo-electron tomography (cryo-ET) allows higher resolution imaging of unfixed cellular samples while preserving architecture, but it requires samples to be vitreous and thin enough for transmission EM. Due to these requirements, cryo-ET has yet to be employed to investigate unfixed, never previously frozen human brain tissue. Here we present a method for generating lamellae in human brain tissue obtained at time of autopsy that can be imaged via cryo-ET. We vitrify the tissue via plunge-freezing and use xenon plasma focused ion beam (FIB) milling to generate lamellae directly on-grid at variable depth inside the tissue. Lamellae generated in Alzheimer's disease brain tissue reveal intact subcellular structures including components of autophagy and potential pathologic tau fibrils. Furthermore, we reveal intact compact myelin and functional cytoplasmic expansions. These images indicate that plasma FIB milling with cryo-ET may be used to elucidate nanoscale structures within the human brain.
History
DepositionJan 10, 2024-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43330.png

Downloads & links

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Map

FileDownload / File: emd_43330.map.gz / Format: CCP4 / Size: 4.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram of human Alzheimer's disease brain tissue
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.7 Å/pix.
x 750 pix.
= 8025. Å		10.7 Å/pix.
x 1440 pix.
= 15408. Å		10.7 Å/pix.
x 1024 pix.
= 10956.8 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: 10.7 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-14420.0 - 8865.0
Average (Standard dev.)289.775359999999978 (±773.319340000000011)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions14401024750
Spacing10241440750
CellA: 10956.8 Å / B: 15408.0 Å / C: 8025.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : human Alzheimer's disease brain tissue

EntireName: human Alzheimer's disease brain tissue
Components
  • Tissue: human Alzheimer's disease brain tissue

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Supramolecule #1: human Alzheimer's disease brain tissue

SupramoleculeName: human Alzheimer's disease brain tissue / type: tissue / ID: 1 / Parent: 0 / Details: middle frontal cortex
Source (natural)Organism: Homo sapiens (human) / Organ: Brain / Tissue: middle frontal cortex

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statetissue

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Sample preparation

BufferpH: 7.4 / Details: DPBS
GridMaterial: COPPER / Mesh: 100
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Chamber temperature: 288 K / Instrument: LEICA EM GP / Details: back blot for 6s before plunging.
Cryo protectant20% glycerol, 1M trehalose
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 7200 / Focused ion beam - Temperature: 113 K / Focused ion beam - Initial thickness: 100000 / Focused ion beam - Final thickness: 350
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Tescan S8000X. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 33000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsRaw images were gain normalize in serialEM. Raw images were high-pass filtered at 1000 pixels then vertical line filtered with a 95% tolerance of direction.
Final reconstructionAlgorithm: BACK PROJECTION / Number images used: 25

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