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- EMDB-51713: High resolution structure of B. oleracea mitoribosome - Large sub... -

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Basic information

Entry
Database: EMDB / ID: EMD-51713
TitleHigh resolution structure of B. oleracea mitoribosome - Large subunit back protuberance focus
Map data
Sample
  • Complex: Full flowering plant mitochondrial ribosome
Keywordsmitochondria / mitoribosome / assembly factor / plant / RIBOSOME
Biological speciesBrassica oleracea var. botrytis (cauliflower)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsWaltz F / Skaltsogiannis V / Giege P
Funding support Germany, Switzerland, 2 items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation Germany
Swiss National Science Foundation210561 Switzerland
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into cauliflower mitoribosome in translation state and in association with a late assembly factor.
Authors: Vasileios Skaltsogiannis / Philippe Wolff / Tan-Trung Nguyen / Nicolas Corre / David Pflieger / Todd Blevins / Yaser Hashem / Philippe Giegé / Florent Waltz /
Abstract: Ribosomes are key molecular machines that translate mRNA into proteins. Mitoribosomes are specific ribosomes found in mitochondria, which have been shown to be remarkably diverse across eukaryotic ...Ribosomes are key molecular machines that translate mRNA into proteins. Mitoribosomes are specific ribosomes found in mitochondria, which have been shown to be remarkably diverse across eukaryotic lineages. In plants, they possess unique features, including additional rRNA domains stabilized by plant-specific proteins. However, the structural specificities of plant mitoribosomes in translation state remained unknown. We used cryo-electron microscopy to provide a high-resolution structural characterization of the cauliflower mitoribosome, in translating and maturation states. The structure reveals the mitoribosome bound with a tRNA in the peptidyl site, along with a segment of mRNA and a nascent polypeptide. Moreover, using structural data, nanopore sequencing and mass spectrometry, we identify a set of 19 ribosomal RNA modifications. Additionally, we observe a late assembly intermediate of the small ribosomal subunit, in complex with the RsgA assembly factor. This reveals how a plant-specific extension of RsgA blocks the mRNA channel to prevent premature mRNA association before complete small subunit maturation. Our findings elucidate key aspects of translation in angiosperm plant mitochondria, revealing its distinct features compared to other eukaryotic lineages.
History
DepositionOct 2, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51713.png

Downloads & links

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Map

FileDownload / File: emd_51713.map.gz / Format: CCP4 / Size: 775.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 588 pix.
= 551.124 Å		0.94 Å/pix.
x 588 pix.
= 551.124 Å		0.94 Å/pix.
x 588 pix.
= 551.124 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.114
Minimum - Maximum-0.65892535 - 1.1010762
Average (Standard dev.)-0.00005853578 (±0.017399775)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions588588588
Spacing588588588
CellA=B=C: 551.12396 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51713_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_51713_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

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Half map: #2

Fileemd_51713_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Full flowering plant mitochondrial ribosome

EntireName: Full flowering plant mitochondrial ribosome
Components
  • Complex: Full flowering plant mitochondrial ribosome

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Supramolecule #1: Full flowering plant mitochondrial ribosome

SupramoleculeName: Full flowering plant mitochondrial ribosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Brassica oleracea var. botrytis (cauliflower)

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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

Concentration3 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 41.66 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 343753
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 219403
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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