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- EMDB-16562: Structure of the yeast delta uL16m mitochondrial ribosome assembl... -

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Basic information

Entry
Database: EMDB / ID: EMD-16562
TitleStructure of the yeast delta uL16m mitochondrial ribosome assembly intermediate - State 1
Map dataState 1, delta uL16m, yeast mitochondrial ribosome, large subunit, consensus map
Sample
  • Complex: Large subunit of the yeast mitochondrial ribosome- State 1, delta uL16m
KeywordsYeast mitochondrial ribosome / delta uL16 / RIBOSOME
Biological speciesSaccharomyces cerevisiae W303 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsConrad J / Rathore S / Barrientos A
Funding support United States, Sweden, Germany, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118141 United States
Swedish Research Council201803694 Sweden
Knut and Alice Wallenberg Foundation2017009 Sweden
German Research Foundation (DFG)SFB860 Germany
CitationJournal: Biochim Biophys Acta Mol Cell Res / Year: 2025
Title: The late stages of yeast mitoribosome large subunit biogenesis.
Authors: Sorbhi Rathore / Julian Conrad / Dasmanthie De Silva / Alberto Ferrari / Danielle Bouquio / Hyung-Jun Kim / Roger Salvatori / Andreas Linden / Olexandr Dybkov / Henning Urlaub / Martin Ott / ...Authors: Sorbhi Rathore / Julian Conrad / Dasmanthie De Silva / Alberto Ferrari / Danielle Bouquio / Hyung-Jun Kim / Roger Salvatori / Andreas Linden / Olexandr Dybkov / Henning Urlaub / Martin Ott / Antoni Barrientos /
Abstract: The Saccharomyces cerevisiae mitoribosome synthesizes eight mitochondrial DNA-encoded proteins essential for oxidative phosphorylation. Mitoribosome large subunit (mtLSU) biogenesis involves the ...The Saccharomyces cerevisiae mitoribosome synthesizes eight mitochondrial DNA-encoded proteins essential for oxidative phosphorylation. Mitoribosome large subunit (mtLSU) biogenesis involves the conserved DEAD-box helicase Mrh4 and the GTPases Mtg1/GTPBP7 and Mtg2/GTPBP5. Here, we have employed genetic, biochemical, in vitro reconstitution, and cryo-EM approaches to elucidate their hierarchical action during the late stages of mtLSU assembly. We show that Mrh4-mediated bL33m incorporation precedes Mtg1 recruitment to the 21S rRNA. Cryo-EM structures of mitoribosome assembly intermediates accumulating in the absence of Mtg1 or uL16m reveal that Mtg1 restructures the 21S rRNA H73-75 and H93 domains to their mature fold. This subsequently allows the structuring of neighboring peptidyl transfer center region helices and the incorporation of uL6m, uL16m, bL35m, and bL36m during late mtLSU maturation. Unexpectedly, monosomes containing immature mtLSU assemble in Mrh4-, bL33m-, uL16m-, Mtg1-, and Mtg2-depleted mitochondria, at levels that increase with the maturation state of the mtLSU particle. Our data have shed light on the rRNA folding events and the structuring of the MRPs that occur during the late stages of assembly. They have provided insight into the roles of assembly factors Mrh4, Mtg1, and Mtg2 during the process and revealed evolutionarily conserved mechanisms underlying mitochondrial ribosome assembly.
History
DepositionJan 27, 2023-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16562.png

Downloads & links

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Map

FileDownload / File: emd_16562.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationState 1, delta uL16m, yeast mitochondrial ribosome, large subunit, consensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.09 Å/pix.
x 360 pix.
= 392.4 Å		1.09 Å/pix.
x 360 pix.
= 392.4 Å		1.09 Å/pix.
x 360 pix.
= 392.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.2
Minimum - Maximum-11.15354 - 19.629411999999999
Average (Standard dev.)-0.000000000005267 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 392.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: State 1, delta uL16m, yeast mitochondrial ribosome, large...

Fileemd_16562_additional_1.map
AnnotationState 1, delta uL16m, yeast mitochondrial ribosome, large subunit, LSU body
Projections & Slices
AxesZYX

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Additional map: State 1, delta uL16m, yeast mitochondrial ribosome, large subunit, CP

Fileemd_16562_additional_2.map
AnnotationState 1, delta uL16m, yeast mitochondrial ribosome, large subunit, CP
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: State 1, delta uL16m, yeast mitochondrial ribosome, large...

Fileemd_16562_additional_3.map
AnnotationState 1, delta uL16m, yeast mitochondrial ribosome, large subunit, E-site tRNA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: State 1, delta uL16m, yeast mitochondrial ribosome, large...

Fileemd_16562_half_map_1.map
AnnotationState 1, delta uL16m, yeast mitochondrial ribosome, large subunit, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: State 1, delta uL16m, yeast mitochondrial ribosome, large...

Fileemd_16562_half_map_2.map
AnnotationState 1, delta uL16m, yeast mitochondrial ribosome, large subunit, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Large subunit of the yeast mitochondrial ribosome- State 1, delta...

EntireName: Large subunit of the yeast mitochondrial ribosome- State 1, delta uL16m
Components
  • Complex: Large subunit of the yeast mitochondrial ribosome- State 1, delta uL16m

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Supramolecule #1: Large subunit of the yeast mitochondrial ribosome- State 1, delta...

SupramoleculeName: Large subunit of the yeast mitochondrial ribosome- State 1, delta uL16m
type: complex / ID: 1 / Parent: 0
Details: Mitoribosomal particles from an uL16m-deletion strain were purified by sucrose cushion sedimentation of mitochondrial extracts prepared in the presence of 20% Mg2+ and 1% Triton X-100. This ...Details: Mitoribosomal particles from an uL16m-deletion strain were purified by sucrose cushion sedimentation of mitochondrial extracts prepared in the presence of 20% Mg2+ and 1% Triton X-100. This approach revealed the structures of novel mitoribosome assembly intermediates. After processing, the structural characterization of the uL16m-deletion mitoribosome particles allowed us to define two major states: state 1, state 2.
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: delta uL16m / Organelle: Mitochondria

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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: EMS Lacey Carbon / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Sample stageCooling holder cryogen: NITROGEN
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:

3551

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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