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- EMDB-65963: In situ subtomogram average of 80S ribosome (local refined with L... -

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Basic information

Entry
Database: EMDB / ID: EMD-65963
TitleIn situ subtomogram average of 80S ribosome (local refined with LSU mask)
Map dataSTA map of Yeast ribosome. Local refined in M with LSU mask.
Sample
  • Complex: Yeast 80S ribosome from cryo-FIB cell lamellae.
KeywordsComplex / In-situ / 80s ribosome / RIBOSOME
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 3.57 Å
AuthorsYang Q / Huang XJ / Zhang XZ
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32325027 China
National Natural Science Foundation of China (NSFC)31930069 China
CitationJournal: Nat Commun / Year: 2026
Title: Ultra-rapid cryo-EM data acquisition method enabled by continuous recording based beam image shift.
Authors: Qi Yang / Xiaojun Huang / Chunling Wu / Yan Zeng / Xinzheng Zhang /
Abstract: Cryo-electron microscopy (cryo-EM) data acquisition is time-intensive given that a large amount of data is required to obtain a high-resolution reconstruction. Here, we eliminate camera-induced delay ...Cryo-electron microscopy (cryo-EM) data acquisition is time-intensive given that a large amount of data is required to obtain a high-resolution reconstruction. Here, we eliminate camera-induced delay time by continuously recording during beam-image shift acquisition using a method called Continuous Recording Beam-Image Shift (CR-BIS). The utilization of CR-BIS with K3 and Falcon 4 direct electron detectors and conventional data acquisition conditions enables the acquisition of ~34,000 micrographs and ~1,000 tilt series per 24 h in single-particle analysis mode and cryo-electron tomography mode, respectively. Three-dimensional reconstructions of single-particle and tomographic datasets show that CR-BIS accelerates data collection and maintains data quality. CR-BIS is broadly applicable for efficient high-resolution cryo-EM since it can be implemented into existing acquisition software through scripting and it does not require hardware modification.
History
DepositionAug 25, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65963.png

Downloads & links

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Map

FileDownload / File: emd_65963.map.gz / Format: CCP4 / Size: 259.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSTA map of Yeast ribosome. Local refined in M with LSU mask.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.57 Å/pix.
x 408 pix.
= 640.56 Å		1.57 Å/pix.
x 408 pix.
= 640.56 Å		1.57 Å/pix.
x 408 pix.
= 640.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.57 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.0086044315 - 0.015916726
Average (Standard dev.)0.0000040412965 (±0.0007552208)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions408408408
Spacing408408408
CellA=B=C: 640.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65963_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Ribosome filtsharp map masked by LSU mask from M.

Fileemd_65963_additional_1.map
AnnotationRibosome filtsharp map masked by LSU mask from M.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Ribosome filtsharp map from M.

Fileemd_65963_additional_2.map
AnnotationRibosome filtsharp map from M.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: STA half map 2 of Yeast ribosome. Local refined in M with LSU mask.

Fileemd_65963_half_map_1.map
AnnotationSTA half map 2 of Yeast ribosome. Local refined in M with LSU mask.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: STA half map 1 of Yeast ribosome. Local refined in M with LSU mask.

Fileemd_65963_half_map_2.map
AnnotationSTA half map 1 of Yeast ribosome. Local refined in M with LSU mask.
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 80S ribosome from cryo-FIB cell lamellae.

EntireName: Yeast 80S ribosome from cryo-FIB cell lamellae.
Components
  • Complex: Yeast 80S ribosome from cryo-FIB cell lamellae.

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Supramolecule #1: Yeast 80S ribosome from cryo-FIB cell lamellae.

SupramoleculeName: Yeast 80S ribosome from cryo-FIB cell lamellae. / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: BY4741

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 4.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 1 / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: M (ver. 2.0.0) / Number subtomograms used: 32527
ExtractionNumber tomograms: 166 / Number images used: 124158 / Software: (Name: Warp (ver. 2.0.0), RELION (ver. 5))
CTF correctionType: NONE
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: M (ver. 2.0.0)
FSC plot (resolution estimation)

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