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- EMDB-69519: Tomogram of mitochondria in T cell from middle-aged patients afte... -

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Basic information

Entry
Database: EMDB / ID: EMD-69519
TitleTomogram of mitochondria in T cell from middle-aged patients after restimulation
Map dataTomogram of mitochondria in T cell from middle-aged patients after restimulation
Sample
  • Organelle or cellular component: Tomogram of mitochondria in T cell from middle-aged patients after restimulation,prepared by cryo-focused ion beam milling of cells
Keywordsmitochondria / T cell / TRANSLATION
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsZhang X / Sang J / Su L / Pan B
Funding support China, 1 items
OrganizationGrant numberCountry
Science and Technology Commission of Shanghai Municipality (STCSM)24QA2705600 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Cryoelectron tomography reveals an age-related decline in mitoribosomes that contributes to T cell dysfunction in older individuals.
Authors: Jingwen Chen / Lili Su / Bangze Pan / Junhao Sang / Linlin Li / Junsong Huang / Zhao-Lan Hu / Lixin Wang / Xiaojie Zhang / Jun Jin /
Abstract: Mitochondrial dysfunction drives T cell aging in mice. Yet, due to fundamental differences in T cell aging mechanisms between species, whether human T cells exhibit similar mitochondrial alterations ...Mitochondrial dysfunction drives T cell aging in mice. Yet, due to fundamental differences in T cell aging mechanisms between species, whether human T cells exhibit similar mitochondrial alterations remains unclear, with existing evidence often conflicting. Using cryoelectron tomography, we resolved the structure and spatial organization of mitochondrial ribosomes in primary human CD8 T cells under physiological conditions. Comparative analysis with human aging models revealed an age-related reduction in mitoribosome abundance and in higher-order mitoribosome organization, which is necessary for cooperative translation. Defective mitochondrial translation suppressed cytosolic ribosomal protein expression, thereby limiting mitochondrial biogenesis. The consequent reduction in mitochondrial mass induced an aged T cell phenotype characterized by compromised memory phenotypes and proliferative capacity. Enhancing mitochondrial translation via overexpression of the mitoribosomal component Mrps5 reversed aged T cell phenotypes in a mouse model of viral infection or tumor. Together, our findings provide nanoscale-resolution views of internal mitochondrial structures in situ, revealing an age-related loss of mitoribosomes. This loss contributes to mitochondrial dysfunction and the subsequent decline in T cell function observed in older individuals. Restoring mitochondrial translation may therefore represent a strategy for mitigating T cell dysfunction in the aging population.
History
DepositionMar 4, 2026-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_69519.png

Downloads & links

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Map

FileDownload / File: emd_69519.map.gz / Format: CCP4 / Size: 2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram of mitochondria in T cell from middle-aged patients after restimulation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.62 Å/pix.
x 500 pix.
= 4808. Å		9.62 Å/pix.
x 1024 pix.
= 9846.784 Å		9.62 Å/pix.
x 1024 pix.
= 9846.784 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: 9.616 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.18911135 - 0.076465674
Average (Standard dev.)0.00001499889 (±0.0039405315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10241024500
Spacing10241024500
CellA: 9846.784 Å / B: 9846.784 Å / C: 4808.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Tomogram of mitochondria in T cell from middle-aged patients afte...

EntireName: Tomogram of mitochondria in T cell from middle-aged patients after restimulation,prepared by cryo-focused ion beam milling of cells
Components
  • Organelle or cellular component: Tomogram of mitochondria in T cell from middle-aged patients after restimulation,prepared by cryo-focused ion beam milling of cells

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Supramolecule #1: Tomogram of mitochondria in T cell from middle-aged patients afte...

SupramoleculeName: Tomogram of mitochondria in T cell from middle-aged patients after restimulation,prepared by cryo-focused ion beam milling of cells
type: organelle_or_cellular_component / 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: 7.5
GridModel: Quantifoil R1/4 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.03 / Focused ion beam - Duration: 3000 / Focused ion beam - Temperature: 77 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 120
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Arctis. 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 130 / Average electron dose: 2.36 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.25 µm / Nominal defocus min: 2.75 µm / Nominal magnification: 53000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: Warp / Number images used: 55
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION

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