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- EMDB-71068: Reconstruction of the yeast 60S ribosomal subunit from CEMOVIS se... -

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Basic information

Entry
Database: EMDB / ID: EMD-71068
TitleReconstruction of the yeast 60S ribosomal subunit from CEMOVIS sections
Map data3D reconstruction calculated from 2DTM results, where the yeast 60S subunit was matched in micrographs from vitreous sections of Saccharomyces cerevisiae cells
Sample
  • Cell: Yeast cells sectioned using CEMOVIS
    • Complex: 60S Ribosomal subunit
KeywordsRibosome CEMOVIS Yeast / TRANSLATION
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsElferich J / Kaminek M / Kong L / Odriozola A / Kukulski W / Zuber B / Grigorieff N
Funding support United States, Switzerland, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Swiss National Science Foundation10000175 Switzerland
CitationJournal: IUCrJ / Year: 2025
Title: In situ high-resolution cryo-EM reconstructions from CEMOVIS.
Authors: Johannes Elferich / Marek Kaminek / Lingli Kong / Adolfo Odriozola / Wanda Kukulski / Benoît Zuber / Nikolaus Grigorieff /
Abstract: Cryo-electron microscopy can be used to image cells and tissue at high resolution. To ensure electron transparency, the sample thickness must not exceed 500 nm. Focused-ion-beam (FIB) milling has ...Cryo-electron microscopy can be used to image cells and tissue at high resolution. To ensure electron transparency, the sample thickness must not exceed 500 nm. Focused-ion-beam (FIB) milling has become the standard method for preparing thin samples (lamellae); however, the material removed by the milling process is lost, the imageable area is usually limited to a few square micrometres and the surface layers sustain damage from the ion beam. We have examined cryo-electron microscopy of vitreous sections (CEMOVIS), a technique based on cutting thin sections with a knife, as an alternative to FIB milling. Vitreous sections also sustain damage, including compression, shearing and cracks. However, samples can be sectioned in series, producing many orders of magnitude more imageable area compared to lamellae, making CEMOVIS an alternative to FIB milling with distinct advantages. Using two-dimensional template matching on images of vitreous sections of Saccharomyces cerevisiae cells, we reconstructed the 60S ribosomal subunit at near-atomic resolution, demonstrating that, in many regions of the sections, the molecular structure of these subunits is largely intact, comparable to FIB-milled lamellae.
History
DepositionJun 6, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71068.png

Downloads & links

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Map

FileDownload / File: emd_71068.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction calculated from 2DTM results, where the yeast 60S subunit was matched in micrographs from vitreous sections of Saccharomyces cerevisiae cells
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 512 pix.
= 599.04 Å		1.17 Å/pix.
x 512 pix.
= 599.04 Å		1.17 Å/pix.
x 512 pix.
= 599.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.17 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-9.498087999999999 - 14.216516499999999
Average (Standard dev.)-0.00505759 (±0.6900153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 599.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-Map 2 of 3D reconstruction calculated from 2DTM...

Fileemd_71068_half_map_1.map
AnnotationHalf-Map 2 of 3D reconstruction calculated from 2DTM results, where the yeast 60S subunit was matched in micrographs from vitreous sections of Saccharomyces cerevisiae cells
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-Map 1 of 3D reconstruction calculated from 2DTM...

Fileemd_71068_half_map_2.map
AnnotationHalf-Map 1 of 3D reconstruction calculated from 2DTM results, where the yeast 60S subunit was matched in micrographs from vitreous sections of Saccharomyces cerevisiae cells
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Yeast cells sectioned using CEMOVIS

EntireName: Yeast cells sectioned using CEMOVIS
Components
  • Cell: Yeast cells sectioned using CEMOVIS
    • Complex: 60S Ribosomal subunit

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Supramolecule #1: Yeast cells sectioned using CEMOVIS

SupramoleculeName: Yeast cells sectioned using CEMOVIS / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #2: 60S Ribosomal subunit

SupramoleculeName: 60S Ribosomal subunit / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.7 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - topology: HOLEY / Support film - #1 - Film thickness: 10
VitrificationCryogen name: NITROGEN / Details: Leica EM PACT2 High Pressure Freezer.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 2 / Number real images: 933 / 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 / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 28238
CTF correctionSoftware - Name: CTFFIND (ver. 5) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6q8y

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 28238
Initial angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 2.5 degrees
Software - Name: cisTEM
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cisTEM

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