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- EMDB-48387: Translational activators Aep1, Aep2 and Atp25 in complex with mRN... -

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Basic information

Entry
Database: EMDB / ID: EMD-48387
TitleTranslational activators Aep1, Aep2 and Atp25 in complex with mRNA and the yeast mitochondrial ribosome
Map dataLocal refined map of translation activator complex (Aep1-Aep2-Atp25) bound to yeast mitoribosomes
Sample
  • Complex: Mitoribosome in complex with translation activator complex (Aep1-Aep2-Atp25C)
Keywordstranslation activator complex / ribosome
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsSherpa D / Shao S
Funding supportEuropean Union, United States, 2 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)European Union
David and Lucile Packard Foundation United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Translational activators align mRNAs at the small mitoribosomal subunit for translation initiation.
Authors: Joseph B Bridgers / Andreas Carlström / Dawafuti Sherpa / Mary T Couvillion / Urška Rovšnik / Jingjing Gao / Bowen Wan / Sichen Shao / Martin Ott / L Stirling Churchman /
Abstract: Mitochondrial gene expression is essential for oxidative phosphorylation. Mitochondrial-encoded mRNAs are translated by dedicated mitochondrial ribosomes (mitoribosomes), whose regulation remains ...Mitochondrial gene expression is essential for oxidative phosphorylation. Mitochondrial-encoded mRNAs are translated by dedicated mitochondrial ribosomes (mitoribosomes), whose regulation remains elusive. In Saccharomyces cerevisiae, nuclear-encoded mitochondrial translational activators (TAs) facilitate transcript-specific translation by a yet unknown mechanism. Here, we investigated the function of TAs containing RNA-binding pentatricopeptide repeats using selective mitoribosome profiling and cryo-electron microscopy (cryo-EM) structural analysis. These analyses show that TAs exhibit strong selectivity for mitoribosomes initiating on their target transcripts. Moreover, TA-mitoribosome footprints indicate that TAs recruit mitoribosomes proximal to the start codon. Two cryo-EM structures of mRNA-TA complexes bound to mitoribosomes stalled in the post-initiation, pre-elongation state revealed the general mechanism of TA action. Specifically, the TAs bind to structural elements in the 5' untranslated region of the client mRNA and the mRNA channel exit to align the mRNA in the small subunit during initiation. Our findings provide a mechanistic basis for understanding how mitochondria achieve transcript-specific translation initiation without relying on general sequence elements to position mitoribosomes at start codons.
History
DepositionDec 20, 2024-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48387.png

Downloads & links

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Map

FileDownload / File: emd_48387.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refined map of translation activator complex (Aep1-Aep2-Atp25) bound to yeast mitoribosomes
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 420 pix.
= 499.8 Å		1.19 Å/pix.
x 420 pix.
= 499.8 Å		1.19 Å/pix.
x 420 pix.
= 499.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.439
Minimum - Maximum-0.9161165 - 1.9974352
Average (Standard dev.)0.002810896 (±0.04563984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 499.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48387_msk_1.map
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Additional map: #1

Fileemd_48387_additional_1.map
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Half map: #2

Fileemd_48387_half_map_1.map
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Half map: #1

Fileemd_48387_half_map_2.map
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Sample components

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Entire : Mitoribosome in complex with translation activator complex (Aep1-...

EntireName: Mitoribosome in complex with translation activator complex (Aep1-Aep2-Atp25C)
Components
  • Complex: Mitoribosome in complex with translation activator complex (Aep1-Aep2-Atp25C)

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Supramolecule #1: Mitoribosome in complex with translation activator complex (Aep1-...

SupramoleculeName: Mitoribosome in complex with translation activator complex (Aep1-Aep2-Atp25C)
type: complex / ID: 1 / Parent: 0
Details: Translational activator complex (Aep1-Aep2-Atp25) bound to yeast mitoribosome
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 48.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25098
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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