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- EMDB-52278: Translational activator Aep3 in complex with mRNA and the yeast m... -

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Basic information

Entry
Database: EMDB / ID: EMD-52278
TitleTranslational activator Aep3 in complex with mRNA and the yeast mitochondrial ribosome (focused on the SSU)
Map data
Sample
  • Complex: Yeast 74S mitochondrial ribosome
    • Complex: 37S mitochondrial ribosome small subunit
    • Complex: 54S mitochondrial ribosome large subunit
KeywordsMitoribosome / translation / RIBOSOME
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsCarlstrom A / Rovsnik U / Ott M
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
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 5, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52278.png

Downloads & links

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Map

FileDownload / File: emd_52278.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 640 pix.
= 529.92 Å		0.83 Å/pix.
x 640 pix.
= 529.92 Å		0.83 Å/pix.
x 640 pix.
= 529.92 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.44057322 - 0.83858377
Average (Standard dev.)0.00019320023 (±0.031923078)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 529.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52278_msk_1.map
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Half map: #1

Fileemd_52278_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_52278_half_map_2.map
Projections & Slices
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Sample components

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Entire : Yeast 74S mitochondrial ribosome

EntireName: Yeast 74S mitochondrial ribosome
Components
  • Complex: Yeast 74S mitochondrial ribosome
    • Complex: 37S mitochondrial ribosome small subunit
    • Complex: 54S mitochondrial ribosome large subunit

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Supramolecule #1: Yeast 74S mitochondrial ribosome

SupramoleculeName: Yeast 74S mitochondrial ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#78
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303

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Supramolecule #2: 37S mitochondrial ribosome small subunit

SupramoleculeName: 37S mitochondrial ribosome small subunit / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#33, #38-#39
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: 54S mitochondrial ribosome large subunit

SupramoleculeName: 54S mitochondrial ribosome large subunit / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #40-#79
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303

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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: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 165000
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: PDB ENTRY
PDB model - PDB ID:

5mrc

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22558
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

5mrc

source_name: PDB, initial_model_type: experimental modelLarge subunit and tRNA in E-site

8om4

source_name: PDB, initial_model_type: experimental modelSmall subunit
source_name: AlphaFold, initial_model_type: in silico modelAep3

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