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- EMDB-39023: Representative tomogram of primary glioblastoma differentiated ce... -

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Entry
Database: EMDB / ID: EMD-39023
TitleRepresentative tomogram of primary glioblastoma differentiated cell with parallel inter-mitochondrial junction.
Map dataRepresentative tomogram of primary glioblastoma differentiated cell with parallel inter-mitochondrial junction.
Sample
  • Cell: Representative tomogram of primary glioblastoma differentiated cell with parallel inter-mitochondrial junction.
KeywordsGlioblastoma differentiated cell / Inter-mitochondrial junction / Mitochondrial clustering / CELL INVASION
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsWang R / Lei H / Wang HX / Qi L / Liu YE / Liu YH / Shi YF / Chen JX / Shen QT
Funding support China, 7 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFF1200400 China
National Science Foundation (NSF, China)32241028 China
National Science Foundation (NSF, China)31800617 China
National Science Foundation (NSF, China)82073274 China
National Science Foundation (NSF, China)82373095 China
National Science Foundation (NSF, China)81872072 China
National Science Foundation (NSF, China)81572501 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Dysregulated inter-mitochondrial crosstalk in glioblastoma cells revealed by in situ cryo-electron tomography.
Authors: Rui Wang / Huan Lei / Hongxiang Wang / Lei Qi / Yu'e Liu / Yunhui Liu / Yufeng Shi / Juxiang Chen / Qing-Tao Shen /
Abstract: Glioblastomas (GBMs) are the most lethal primary brain tumors with limited survival, even under aggressive treatments. The current therapeutics for GBMs are flawed due to the failure to accurately ...Glioblastomas (GBMs) are the most lethal primary brain tumors with limited survival, even under aggressive treatments. The current therapeutics for GBMs are flawed due to the failure to accurately discriminate between normal proliferating cells and distinctive tumor cells. Mitochondria are essential to GBMs and serve as potential therapeutical targets. Here, we utilize cryo-electron tomography to quantitatively investigate nanoscale details of randomly sampled mitochondria in their native cellular context of GBM cells. Our results show that compared with cancer-free brain cells, GBM cells own more inter-mitochondrial junctions of several types for communications. Furthermore, our tomograms unveil microtubule-dependent mitochondrial nanotunnel-like bridges in the GBM cells as another inter-mitochondrial structure. These quantified inter-mitochondrial features, together with other mitochondria-organelle and intra-mitochondrial ones, are sufficient to distinguish GBM cells from cancer-free brain cells under scrutiny with predictive modeling. Our findings decipher high-resolution inter-mitochondrial structural signatures and provide clues for diagnosis and therapeutic interventions for GBM and other mitochondria-related diseases.
History
DepositionFeb 4, 2024-
Header (metadata) releaseMar 20, 2024-
Map releaseMar 20, 2024-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39023.png

Downloads & links

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Map

FileDownload / File: emd_39023.map.gz / Format: CCP4 / Size: 297.4 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationRepresentative tomogram of primary glioblastoma differentiated cell with parallel inter-mitochondrial junction.
Voxel sizeX=Y=Z: 29.04 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)-64.499120000000005 (±109.786680000000004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin17500
Dimensions928960350
Spacing960928350
CellA: 27878.4 Å / B: 26949.121 Å / C: 10164.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Representative tomogram of primary glioblastoma differentiated ce...

EntireName: Representative tomogram of primary glioblastoma differentiated cell with parallel inter-mitochondrial junction.
Components
  • Cell: Representative tomogram of primary glioblastoma differentiated cell with parallel inter-mitochondrial junction.

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Supramolecule #1: Representative tomogram of primary glioblastoma differentiated ce...

SupramoleculeName: Representative tomogram of primary glioblastoma differentiated cell with parallel inter-mitochondrial junction.
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Ted Pella / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 15.0 µm / Nominal defocus min: 5.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.9 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 41

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