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- EMDB-16590: Structure of the yeast delta uL16m mitochondrial ribosome - State 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-16590
TitleStructure of the yeast delta uL16m mitochondrial ribosome - State 2
Map dataconsensus map of delta uL16m yeast mitochondrial ribosome- State2
Sample
  • Complex: Structure of the yeast delta uL16m mitochondrial ribosome - State 2
KeywordsStructure of the yeast delta uL16m mitochondrial ribosome / 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 31, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16590.png

Downloads & links

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Map

FileDownload / File: emd_16590.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationconsensus map of delta uL16m yeast mitochondrial ribosome- State2
Projections & slices

Image control

Size
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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: 3.0
Minimum - Maximum-6.039334 - 14.381447
Average (Standard dev.)-0.000000000000612 (±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: Multibody refinement of delta uL16m yeast mitochondrial SSU body

Fileemd_16590_additional_1.map
AnnotationMultibody refinement of delta uL16m yeast mitochondrial SSU body
Projections & Slices
AxesZYX

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Additional map: Multibody refinement of delta uL16m yeast mitochondrial SSU head

Fileemd_16590_additional_2.map
AnnotationMultibody refinement of delta uL16m yeast mitochondrial SSU head
Projections & Slices
AxesZYX

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Additional map: Multibody refinement of delta uL16m yeast mitochondrial LSU

Fileemd_16590_additional_3.map
AnnotationMultibody refinement of delta uL16m yeast mitochondrial LSU
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_16590_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_16590_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of the yeast delta uL16m mitochondrial ribosome - State 2

EntireName: Structure of the yeast delta uL16m mitochondrial ribosome - State 2
Components
  • Complex: Structure of the yeast delta uL16m mitochondrial ribosome - State 2

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Supramolecule #1: Structure of the yeast delta uL16m mitochondrial ribosome - State 2

SupramoleculeName: Structure of the yeast delta uL16m mitochondrial ribosome - State 2
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 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / 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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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: 25000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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