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- EMDB-24291: Cryo-ET platelet of control mouse (1 week) -

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Basic information

Entry
Database: EMDB / ID: EMD-24291
TitleCryo-ET platelet of control mouse (1 week)
Map dataRepresentative tomographic reconstruction of platelet from control mouse(1 week). Bin4.
Sample
  • Cell: Platelet of control mouse (1 week)
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsHuo T / Wang Z
CitationJournal: Commun Biol / Year: 2022
Title: Using Cryo-ET to distinguish platelets during pre-acute myeloid leukemia from steady state hematopoiesis.
Authors: Yuewei Wang / Tong Huo / Yu-Jung Tseng / Lan Dang / Zhili Yu / Wenjuan Yu / Zachary Foulks / Rebecca L Murdaugh / Steven J Ludtke / Daisuke Nakada / Zhao Wang /
Abstract: Early diagnosis of acute myeloid leukemia (AML) in the pre-leukemic stage remains a clinical challenge, as pre-leukemic patients show no symptoms, lacking any known morphological or numerical ...Early diagnosis of acute myeloid leukemia (AML) in the pre-leukemic stage remains a clinical challenge, as pre-leukemic patients show no symptoms, lacking any known morphological or numerical abnormalities in blood cells. Here, we demonstrate that platelets with structurally abnormal mitochondria emerge at the pre-leukemic phase of AML, preceding detectable changes in blood cell counts or detection of leukemic blasts in blood. We visualized frozen-hydrated platelets from mice at different time points during AML development in situ using electron cryo-tomography (cryo-ET) and identified intracellular organelles through an unbiased semi-automatic process followed by quantitative measurement. A large proportion of platelets exhibited changes in the overall shape and depletion of organelles in AML. Notably, 23% of platelets in pre-leukemic cells exhibit abnormal, round mitochondria with unfolded cristae, accompanied by a significant drop in ATP levels and altered expression of metabolism-related gene signatures. Our study demonstrates that detectable structural changes in pre-leukemic platelets may serve as a biomarker for the early diagnosis of AML.
History
DepositionJun 24, 2021-
Header (metadata) releaseFeb 23, 2022-
Map releaseFeb 23, 2022-
UpdateFeb 23, 2022-
Current statusFeb 23, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Movie viewer
Supplemental images

emd_24291.png

Downloads & links

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Map

FileDownload / File: emd_24291.map.gz / Format: CCP4 / Size: 2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRepresentative tomographic reconstruction of platelet from control mouse(1 week). Bin4.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
48.24 Å/pix.
x 576 pix.
= 27786.24 Å		48.24 Å/pix.
x 960 pix.
= 46310.402 Å		48.24 Å/pix.
x 960 pix.
= 46310.402 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: 48.24 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-80.30583 - 27.272259
Average (Standard dev.)1.1769025e-08 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-480-480-288
Dimensions960960576
Spacing960960576
CellA: 46310.402 Å / B: 46310.402 Å / C: 27786.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z48.24000208333348.24000208333348.24
M x/y/z960960576
origin x/y/z0.0000.0000.000
length x/y/z46310.40246310.40227786.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-480-480-288
NC/NR/NS960960576
D min/max/mean-80.30627.2720.000

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Supplemental data

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Sample components

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Entire : Platelet of control mouse (1 week)

EntireName: Platelet of control mouse (1 week)
Components
  • Cell: Platelet of control mouse (1 week)

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Supramolecule #1: Platelet of control mouse (1 week)

SupramoleculeName: Platelet of control mouse (1 week) / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: AURION / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 31

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