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- EMDB-50765: Drosophila melanogaster Ovaries 80S ribosome vacant (Class 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-50765
TitleDrosophila melanogaster Ovaries 80S ribosome vacant (Class 1)
Map datamain
Sample
  • Complex: Vacant 80S ribosome
KeywordsRibosome / D. melanogaster / Ovary
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.97 Å
AuthorsBlandy A / Hopes T / Vasconcelos EJR / Turner A / Fatkhullin B / Agapiou M / Fontana J / Aspden JL
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Translational activity of 80S monosomes varies dramatically across different tissues.
Authors: Albert Blandy / Tayah Hopes / Elton J R Vasconcelos / Amy Turner / Bulat Fatkhullin / Michaela Agapiou / Juan Fontana / Julie L Aspden /
Abstract: Translational regulation at the stage of initiation can impact the number of ribosomes translating each mRNA molecule. However, the translational activity of single 80S ribosomes (monosomes) on mRNA ...Translational regulation at the stage of initiation can impact the number of ribosomes translating each mRNA molecule. However, the translational activity of single 80S ribosomes (monosomes) on mRNA is less well understood, even though these 80S monosomes represent the dominant ribosomal complexes in vivo. Here, we used cryo-EM to determine the translational activity of 80S monosomes across different tissues in Drosophila melanogaster. We discovered that while head and embryo 80S monosomes are highly translationally active, testis and ovary 80S monosomes are translationally inactive. RNA-Seq analysis of head monosome- and polysome-translated mRNAs, revealed that head 80S monosomes preferentially translate mRNAs with TOP motifs, short 5'-UTRs, short ORFs and are enriched for the presence of uORFs. Overall, these findings highlight that regulation of translation initiation and protein synthesis is mostly performed by monosomes in head and embryo, while polysomes are the main source of protein production in testis and ovary.
History
DepositionJun 26, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50765.png

Downloads & links

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Map

FileDownload / File: emd_50765.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.35 Å/pix.
x 80 pix.
= 428. Å		5.35 Å/pix.
x 80 pix.
= 428. Å		5.35 Å/pix.
x 80 pix.
= 428. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 5.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0311
Minimum - Maximum-0.0787015 - 0.24272959
Average (Standard dev.)0.0011719669 (±0.028235434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 428.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half1

Fileemd_50765_half_map_1.map
Annotationhalf1
Projections & Slices
AxesZYX

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Half map: half2

Fileemd_50765_half_map_2.map
Annotationhalf2
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Histogram (log scale)

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Sample components

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Entire : Vacant 80S ribosome

EntireName: Vacant 80S ribosome
Components
  • Complex: Vacant 80S ribosome

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Supramolecule #1: Vacant 80S ribosome

SupramoleculeName: Vacant 80S ribosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 82.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 80480
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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