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- EMDB-50493: LSU structure derived from the monosome sample of the mitoribosom... -

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Basic information

Entry
Database: EMDB / ID: EMD-50493
TitleLSU structure derived from the monosome sample of the mitoribosome from T. gondii.
Map dataDeepEMhanced map of the LSU structure derived from the monosome sample of the mitoribosome from T. gondii.
Sample
  • Complex: LSU structure derived from the LSU sample of the mitoribosome from T. gondii.
KeywordsComplex / translation / rRNA / RIBOSOME
Biological speciesToxoplasma gondii (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsRocha REO / Barua S / Boissier F / Nguyen TT / Hashem Y
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Commission101088541European Union
CitationJournal: Nat Commun / Year: 2024
Title: Apicomplexan mitoribosome from highly fragmented rRNAs to a functional machine.
Authors: Chaoyue Wang / Sari Kassem / Rafael Eduardo Oliveira Rocha / Pei Sun / Tan-Trung Nguyen / Joachim Kloehn / Xianyong Liu / Lorenzo Brusini / Alessandro Bonavoglia / Sramona Barua / Fanny ...Authors: Chaoyue Wang / Sari Kassem / Rafael Eduardo Oliveira Rocha / Pei Sun / Tan-Trung Nguyen / Joachim Kloehn / Xianyong Liu / Lorenzo Brusini / Alessandro Bonavoglia / Sramona Barua / Fanny Boissier / Mayara Lucia Del Cistia / Hongjuan Peng / Xinming Tang / Fujie Xie / Zixuan Wang / Oscar Vadas / Xun Suo / Yaser Hashem / Dominique Soldati-Favre / Yonggen Jia /
Abstract: The phylum Apicomplexa comprises eukaryotic parasites that cause fatal diseases affecting millions of people and animals worldwide. Their mitochondrial genomes have been significantly reduced, ...The phylum Apicomplexa comprises eukaryotic parasites that cause fatal diseases affecting millions of people and animals worldwide. Their mitochondrial genomes have been significantly reduced, leaving only three protein-coding genes and highly fragmented mitoribosomal rRNAs, raising challenging questions about mitoribosome composition, assembly and structure. Our study reveals how Toxoplasma gondii assembles over 40 mt-rRNA fragments using exclusively nuclear-encoded mitoribosomal proteins and three lineage-specific families of RNA-binding proteins. Among these are four proteins from the Apetala2/Ethylene Response Factor (AP2/ERF) family, originally known as transcription factors in plants and Apicomplexa, now repurposed as essential mitoribosome components. Cryo-EM analysis of the mitoribosome structure demonstrates how these AP2 proteins function as RNA binders to maintain mitoribosome integrity. The mitoribosome is also decorated with members of lineage-specific RNA-binding proteins belonging to RAP (RNA-binding domain abundant in Apicomplexa) proteins and HPR (heptatricopeptide repeat) families, highlighting the unique adaptations of these parasites. Solving the molecular puzzle of apicomplexan mitoribosome could inform the development of therapeutic strategies targeting organellar translation.
History
DepositionMay 29, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50493.png

Downloads & links

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Map

FileDownload / File: emd_50493.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhanced map of the LSU structure derived from the monosome sample of the mitoribosome from T. gondii.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.51 Å/pix.
x 420 pix.
= 632.394 Å		1.51 Å/pix.
x 420 pix.
= 632.394 Å		1.51 Å/pix.
x 420 pix.
= 632.394 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5057 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.125
Minimum - Maximum-0.039153017 - 2.3172276
Average (Standard dev.)0.0015733518 (±0.02791459)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 632.394 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50493_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map of the LSU structure derived from...

Fileemd_50493_additional_1.map
AnnotationSharpened map of the LSU structure derived from the monosome sample of the mitoribosome from T. gondii.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of the LSU structure derived...

Fileemd_50493_half_map_1.map
AnnotationHalf map A of the LSU structure derived from the monosome sample of the mitoribosome from T. gondii.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of the LSU structure derived...

Fileemd_50493_half_map_2.map
AnnotationHalf map B of the LSU structure derived from the monosome sample of the mitoribosome from T. gondii.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LSU structure derived from the LSU sample of the mitoribosome fro...

EntireName: LSU structure derived from the LSU sample of the mitoribosome from T. gondii.
Components
  • Complex: LSU structure derived from the LSU sample of the mitoribosome from T. gondii.

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Supramolecule #1: LSU structure derived from the LSU sample of the mitoribosome fro...

SupramoleculeName: LSU structure derived from the LSU sample of the mitoribosome from T. gondii.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11, #13-#22, #24-#25, #27
Source (natural)Organism: Toxoplasma gondii (eukaryote) / Organelle: Mitochondria / Location in cell: Cytoplasm
Molecular weightTheoretical: 4 MDa

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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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 2.6e-05 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting force 5, blotting time 2.5 seconds..

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
TemperatureMin: 90.0 K / Max: 95.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 9524 / Average exposure time: 6.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 211474
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 211474
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationNumber classes: 4 / Avg.num./class: 70000 / Software - Name: cryoSPARC (ver. 4.5.1) / Software - details: Heterogeneous refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL

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