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- EMDB-64899: human mitoirbosome trapped by retapamulin, global map -

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Basic information

Entry
Database: EMDB / ID: EMD-64899
Titlehuman mitoirbosome trapped by retapamulin, global map
Map data
Sample
  • Complex: human mitoribosome trapped by retapamulin
Keywordsmitoribosome / retapamulin / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsAndo Y / Nureki O / Itoh Y
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR20E2 Japan
Japan Society for the Promotion of Science (JSPS)JP25KJ0893 Japan
CitationJournal: Mol Cell / Year: 2025
Title: Monitoring the complexity and dynamics of mitochondrial translation.
Authors: Taisei Wakigawa / Mari Mito / Yushin Ando / Haruna Yamashiro / Kotaro Tomuro / Haruna Tani / Kazuhito Tomizawa / Takeshi Chujo / Asuteka Nagao / Takeo Suzuki / Osamu Nureki / Fan-Yan Wei / ...Authors: Taisei Wakigawa / Mari Mito / Yushin Ando / Haruna Yamashiro / Kotaro Tomuro / Haruna Tani / Kazuhito Tomizawa / Takeshi Chujo / Asuteka Nagao / Takeo Suzuki / Osamu Nureki / Fan-Yan Wei / Yuichi Shichino / Yuzuru Itoh / Tsutomu Suzuki / Shintaro Iwasaki /
Abstract: Since mitochondrial translation leads to the synthesis of the essential oxidative phosphorylation (OXPHOS) subunits, exhaustive and quantitative delineation of mitoribosome traversal is needed. Here, ...Since mitochondrial translation leads to the synthesis of the essential oxidative phosphorylation (OXPHOS) subunits, exhaustive and quantitative delineation of mitoribosome traversal is needed. Here, we developed a variety of high-resolution mitochondrial ribosome profiling derivatives and revealed the intricate regulation of mammalian mitochondrial translation. Harnessing a translation inhibitor, retapamulin, our approach assessed the stoichiometry and kinetics of mitochondrial translation flux, such as the number of mitoribosomes on a transcript, the elongation rate, and the initiation rate. We also surveyed the impacts of modifications at the anticodon stem loop in mitochondrial tRNAs (mt-tRNAs), including all possible modifications at the 34th position, in cells deleting the corresponding enzymes and derived from patients, as well as in mouse tissues. Moreover, a retapamulin-assisted derivative and mito-disome profiling revealed mitochondrial translation initiation factor (mtIF) 3-mediated translation initiation from internal open reading frames (ORFs) and programmed mitoribosome collision sites across the mitochondrial transcriptome. Our work provides a useful platform for investigating protein synthesis within the energy powerhouse of the cell.
History
DepositionJun 2, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64899.png

Downloads & links

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Map

FileDownload / File: emd_64899.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.10669794 - 0.29472533
Average (Standard dev.)0.00004882305 (±0.014153196)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64899_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64899_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human mitoribosome trapped by retapamulin

EntireName: human mitoribosome trapped by retapamulin
Components
  • Complex: human mitoribosome trapped by retapamulin

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Supramolecule #1: human mitoribosome trapped by retapamulin

SupramoleculeName: human mitoribosome trapped by retapamulin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#86
Source (natural)Organism: Homo sapiens (human)

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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
GridModel: Quantifoil R2/1 / Material: GOLD / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
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: EMDB MAP
EMDB ID:

2876

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 114776
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION

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