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- EMDB-52408: Mouse mitochondrial large subunit assembly intermediate in comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-52408
TitleMouse mitochondrial large subunit assembly intermediate in complex with MRM2 dimer with uL16m bound (SAMC Knock-out)
Map dataunsharpened map
Sample
  • Complex: Mouse mitochondrial large subunit intermediate
KeywordsMitochondria / ribosome / large subunit / assembly
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.42 Å
AuthorsSingh V / Rorbach J / Freyer C / Wredenberg A
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat Commun / Year: 2025
Title: The mitochondrial methylation potential gates mitoribosome assembly.
Authors: Ruth I C Glasgow / Vivek Singh / Lucía Peña-Pérez / Alissa Wilhalm / Marco F Moedas / David Moore / Florian A Rosenberger / Xinping Li / Ilian Atanassov / Mira Saba / Miriam Cipullo / ...Authors: Ruth I C Glasgow / Vivek Singh / Lucía Peña-Pérez / Alissa Wilhalm / Marco F Moedas / David Moore / Florian A Rosenberger / Xinping Li / Ilian Atanassov / Mira Saba / Miriam Cipullo / Joanna Rorbach / Anna Wedell / Christoph Freyer / Alexey Amunts / Anna Wredenberg /
Abstract: S-adenosylmethionine (SAM) is the principal methyl donor in cells and is essential for mitochondrial gene expression, influencing RNA modifications, translation, and ribosome biogenesis. Using direct ...S-adenosylmethionine (SAM) is the principal methyl donor in cells and is essential for mitochondrial gene expression, influencing RNA modifications, translation, and ribosome biogenesis. Using direct long-read RNA sequencing in mouse tissues and embryonic fibroblasts, we show that processing of the mitochondrial ribosomal gene cluster fails in the absence of mitochondrial SAM, leading to an accumulation of unprocessed precursors. Proteomic analysis of ribosome fractions revealed these precursors associated with processing and assembly factors, indicating stalled biogenesis. Structural analysis by cryo-electron microscopy demonstrated that SAM-dependent methylation is required for peptidyl transferase centre formation during mitoribosome assembly. Our findings identify a critical role for SAM in coordinating mitoribosomal RNA processing and large subunit maturation, linking cellular methylation potential to mitochondrial translation capacity.
History
DepositionDec 21, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52408.png

Downloads & links

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Map

FileDownload / File: emd_52408.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 540 pix.
= 456.84 Å		0.85 Å/pix.
x 540 pix.
= 456.84 Å		0.85 Å/pix.
x 540 pix.
= 456.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.846 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.18454069 - 0.4488239
Average (Standard dev.)0.0021260711 (±0.028030494)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 456.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52408_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52408_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mouse mitochondrial large subunit intermediate

EntireName: Mouse mitochondrial large subunit intermediate
Components
  • Complex: Mouse mitochondrial large subunit intermediate

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Supramolecule #1: Mouse mitochondrial large subunit intermediate

SupramoleculeName: Mouse mitochondrial large subunit intermediate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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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: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5040
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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