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- EMDB-18169: Composite map of the Gallus gallus 80S rotated ribosome in comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-18169
TitleComposite map of the Gallus gallus 80S rotated ribosome in complex with eEF2 and SERBP1
Map dataComposite map of the Gallus gallus 80S rotated ribosome in complex with eEF2 and SERBP1
Sample
  • Complex: 80S Gallus gallus ribosome from chicken embryo
Keywordstranslation / complex / eEF2 / SERBP1 / RIBOSOME
Biological speciesGallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsNurullina L / Jenner L / Myasnikov A / Yusupov M
Funding support France, 1 items
OrganizationGrant numberCountry
Fondation pour la Recherche Medicale (FRM) France
CitationJournal: To Be Published
Title: Structural insights into inactive ribosome complexes derived from cold-treated chick embryo cells
Authors: Nurullina L / Terrosu S / Jenner L / Myasnikov A / Yusupov M
History
DepositionAug 8, 2023-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18169.png

Downloads & links

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Map

FileDownload / File: emd_18169.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of the Gallus gallus 80S rotated ribosome in complex with eEF2 and SERBP1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (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: 3.0
Minimum - Maximum-17.913443000000001 - 35.597855000000003
Average (Standard dev.)-0.001120761 (±1.0801704)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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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 reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: OTHER / Software - Name: cryoSPARC / Details: Composite map / Number images used: 100204
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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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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