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- EMDB-18160: Focused map of the 40S ribosomal subunit body of the Gallus gallu... -

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Basic information

Entry
Database: EMDB / ID: EMD-18160
TitleFocused map of the 40S ribosomal subunit body of the Gallus gallus (rotated)
Map dataFocused map of the 40S ribosomal subunit body of the Gallus gallus (rotated)
Sample
  • Complex: 80S Gallus gallus ribosome from chicken embryo
Keywordstranslation / complex / eEF2 / SERBP1 / RIBOSOME
Biological speciesGallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsNurullina L / Jenner L / Myasnikov A / Yusupov M
Funding support France, 1 items
OrganizationGrant numberCountry
Fondation pour la Recherche Medicale (FRM) France
CitationJournal: FEBS Lett / Year: 2024
Title: Cryo-EM structure of the inactive ribosome complex accumulated in chick embryo cells in cold-stress conditions.
Authors: Liliia Nurullina / Salvatore Terrosu / Alexander G Myasnikov / Lasse Bohl Jenner / Marat Yusupov /
Abstract: Here, we present the high-resolution structure of the Gallus gallus 80S ribosome obtained from cold-treated chicken embryos. The translationally inactive ribosome complex contains elongation factor ...Here, we present the high-resolution structure of the Gallus gallus 80S ribosome obtained from cold-treated chicken embryos. The translationally inactive ribosome complex contains elongation factor eEF2 with GDP, SERPINE1 mRNA binding protein 1 (SERBP1) and deacylated tRNA in the P/E position, showing common features with complexes already described in mammals. Modeling of most expansion segments of G. gallus 28S ribosomal RNA allowed us to identify specific features in their structural organization and to describe areas where a marked difference between mammalian and avian ribosomes could shed light on the evolution of the expansion segments. This study provides the first structure of an avian ribosome, establishing a model for future structural and functional studies on the translational machinery in Aves.
History
DepositionAug 8, 2023-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18160.png

Downloads & links

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Map

FileDownload / File: emd_18160.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of the 40S ribosomal subunit body of the Gallus gallus (rotated)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 580 pix.
= 465.74 Å		0.8 Å/pix.
x 580 pix.
= 465.74 Å		0.8 Å/pix.
x 580 pix.
= 465.74 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.803 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.43942174 - 0.97440255
Average (Standard dev.)-0.0023263684 (±0.020585764)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions580580580
Spacing580580580
CellA=B=C: 465.74 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map 1

Fileemd_18160_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_18160_half_map_2.map
AnnotationHalf-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 : 80S Gallus gallus ribosome from chicken embryo

EntireName: 80S Gallus gallus ribosome from chicken embryo
Components
  • Complex: 80S Gallus gallus ribosome from chicken embryo

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Supramolecule #1: 80S Gallus gallus ribosome from chicken embryo

SupramoleculeName: 80S Gallus gallus ribosome from chicken embryo / type: complex / ID: 1 / Parent: 0
Details: 28S rRNA, 5.8S rRNA, 5S rRNA, 18S rRNA,ribosomal proteins, tRNA, eEF2, SERBP1
Source (natural)Organism: Gallus gallus (chicken) / Tissue: embryo
Molecular weightTheoretical: 4.3 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
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 32439 / 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 / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 641721
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7o7z

Final reconstructionNumber classes used: 2 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Software - Name: cryoSPARC / Number images used: 100204
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7o7z


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation coefficient

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