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- EMDB-65576: In situ structure of S. pombe 80S ribosome -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-65576
TitleIn situ structure of S. pombe 80S ribosome
Map data
Sample
  • Cell: cryo-FIB-milled lamellae of wild-type S. pombe
Keywords80S ribosome / RIBOSOME
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 7.46 Å
AuthorsLuo ZW / Wang QH / Ma JP
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: OPUS-TOMO: Towards Resolving Dynamics and Compositional Heterogeneities of Biomolecules with Cryo-Electron Tomography
Authors: Luo ZW / Wang QH / Ma JP
History
DepositionJul 28, 2025-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65576.png

Downloads & links

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Map

FileDownload / File: emd_65576.map.gz / Format: CCP4 / Size: 26.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.37 Å/pix.
x 190 pix.
= 640.3 Å		3.37 Å/pix.
x 190 pix.
= 640.3 Å		3.37 Å/pix.
x 190 pix.
= 640.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.022418253 - 0.047784097
Average (Standard dev.)0.00017464216 (±0.0027131373)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions190190190
Spacing190190190
CellA=B=C: 640.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65576_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65576_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65576_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : cryo-FIB-milled lamellae of wild-type S. pombe

EntireName: cryo-FIB-milled lamellae of wild-type S. pombe
Components
  • Cell: cryo-FIB-milled lamellae of wild-type S. pombe

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Supramolecule #1: cryo-FIB-milled lamellae of wild-type S. pombe

SupramoleculeName: cryo-FIB-milled lamellae of wild-type S. pombe / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)

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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: 7
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.4 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 / Nominal magnification: 42000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: M / Number subtomograms used: 17215
ExtractionNumber tomograms: 10 / Number images used: 50000 / Software - Name: Warp
CTF correctionSoftware - Name: M / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: M
FSC plot (resolution estimation)

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