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- EMDB-17095: Small subunit of yeast mitochondrial ribosome in complex with IF3... -

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Basic information

Entry
Database: EMDB / ID: EMD-17095
TitleSmall subunit of yeast mitochondrial ribosome in complex with IF3/Aim23 (local-masked refined on the body)
Map data
Sample
  • Complex: Small subunit of mitochondrial ribosome in complex with IF3/Aim23
Keywordsmitochondria / initiation factor 3 / pre-initiation complex / mtIF3 / RIBOSOME
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsItoh Y / Chicherin I / Kamenski P / Amunts A
Funding supportEuropean Union, Sweden, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2018-StG-805230European Union
The Swedish Foundation for Strategic ResearchFFL15:0325 Sweden
CitationJournal: Mol Cell / Year: 2024
Title: METTL17 is an Fe-S cluster checkpoint for mitochondrial translation.
Authors: Tslil Ast / Yuzuru Itoh / Shayan Sadre / Jason G McCoy / Gil Namkoong / Jordan C Wengrod / Ivan Chicherin / Pallavi R Joshi / Piotr Kamenski / Daniel L M Suess / Alexey Amunts / Vamsi K Mootha /
Abstract: Friedreich's ataxia (FA) is a debilitating, multisystemic disease caused by the depletion of frataxin (FXN), a mitochondrial iron-sulfur (Fe-S) cluster biogenesis factor. To understand the cellular ...Friedreich's ataxia (FA) is a debilitating, multisystemic disease caused by the depletion of frataxin (FXN), a mitochondrial iron-sulfur (Fe-S) cluster biogenesis factor. To understand the cellular pathogenesis of FA, we performed quantitative proteomics in FXN-deficient human cells. Nearly every annotated Fe-S cluster-containing protein was depleted, indicating that as a rule, cluster binding confers stability to Fe-S proteins. We also observed depletion of a small mitoribosomal assembly factor METTL17 and evidence of impaired mitochondrial translation. Using comparative sequence analysis, mutagenesis, biochemistry, and cryoelectron microscopy, we show that METTL17 binds to the mitoribosomal small subunit during late assembly and harbors a previously unrecognized [FeS] cluster required for its stability. METTL17 overexpression rescued the mitochondrial translation and bioenergetic defects, but not the cellular growth, of FXN-depleted cells. These findings suggest that METTL17 acts as an Fe-S cluster checkpoint, promoting translation of Fe-S cluster-rich oxidative phosphorylation (OXPHOS) proteins only when Fe-S cofactors are replete.
History
DepositionApr 11, 2023-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17095.png

Downloads & links

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Map

FileDownload / File: emd_17095.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.018717648 - 0.068924926
Average (Standard dev.)-0.000056021086 (±0.002218356)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 398.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17095_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17095_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17095_half_map_2.map
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 : Small subunit of mitochondrial ribosome in complex with IF3/Aim23

EntireName: Small subunit of mitochondrial ribosome in complex with IF3/Aim23
Components
  • Complex: Small subunit of mitochondrial ribosome in complex with IF3/Aim23

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Supramolecule #1: Small subunit of mitochondrial ribosome in complex with IF3/Aim23

SupramoleculeName: Small subunit of mitochondrial ribosome in complex with IF3/Aim23
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#35
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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
Component:
ConcentrationFormulaName
50.0 mMKClpotassium chloride
20.0 mMHEPES-KOH buffer pH7.5
5.0 mMmagnesium acetate
2.0 mMdithiothreitol
0.05 %n-dodecyl-beta-D-maltoside
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 40 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

3551

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53922
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5mrc


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL

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