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- EMDB-69523: In-cell map of mitoribosome from T cells of older patients after ... -

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Basic information

Entry
Database: EMDB / ID: EMD-69523
TitleIn-cell map of mitoribosome from T cells of older patients after restimulation by subtomogram averaging
Map dataIn-cell map of mitoribosome from T cells of older patients after restimulation by subtomogram averaging
Sample
  • Complex: mitoribosome from T cells of older patients after restimulation, prepared by cryo-focused ion beam milling of cells
Keywordsmitoribosome / mitochondria / T cell / TRANSLATION
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 26.0 Å
AuthorsZhang X / Pan B / Su L / Sang J
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_69523.png

Downloads & links

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Map

FileDownload / File: emd_69523.map.gz / Format: CCP4 / Size: 549.8 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn-cell map of mitoribosome from T cells of older patients after restimulation by subtomogram averaging
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.62 Å/pix.
x 52 pix.
= 500.032 Å		9.62 Å/pix.
x 52 pix.
= 500.032 Å		9.62 Å/pix.
x 52 pix.
= 500.032 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 9.616 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.63
Minimum - Maximum-1.6889949 - 3.1432958
Average (Standard dev.)0.03732216 (±0.47544277)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions525252
Spacing525252
CellA=B=C: 500.032 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_69523_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: In-cell halfmap1 of mitoribosome from T cells of...

Fileemd_69523_half_map_1.map
AnnotationIn-cell halfmap1 of mitoribosome from T cells of older patients after restimulation by subtomogram averaging
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: In-cell halfmap2 of mitoribosome from T cells of...

Fileemd_69523_half_map_2.map
AnnotationIn-cell halfmap2 of mitoribosome from T cells of older patients after restimulation by subtomogram averaging
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mitoribosome from T cells of older patients after restimulation, ...

EntireName: mitoribosome from T cells of older patients after restimulation, prepared by cryo-focused ion beam milling of cells
Components
  • Complex: mitoribosome from T cells of older patients after restimulation, prepared by cryo-focused ion beam milling of cells

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Supramolecule #1: mitoribosome from T cells of older patients after restimulation, ...

SupramoleculeName: mitoribosome from T cells of older patients after restimulation, prepared by cryo-focused ion beam milling of cells
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1/4 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP
DetailsSpecimen prepared by cryo-focused ion beam milling of cells

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / 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 reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 155
ExtractionNumber tomograms: 10 / Number images used: 3000 / Software - Name: Warp
CTF correctionSoftware - Name: Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model

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