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- EMDB-56855: Cryo-EM structure of yeast ribosome solved with EasyGrid -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-56855
TitleCryo-EM structure of yeast ribosome solved with EasyGrid
Map data
Sample
  • Complex: Cryo-EM structure of yeast ribosome solved with EasyGrid
KeywordsYeast / ribosome / cryo-EM SPA
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.43 Å
AuthorsGemin O / Papp G
Funding support Germany, 1 items
OrganizationGrant numberCountry
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of yeast ribosome solved with EasyGrid
Authors: Gemin O / Papp G
History
DepositionFeb 20, 2026-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56855.png

Downloads & links

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Map

FileDownload / File: emd_56855.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 600 pix.
= 438. Å		0.73 Å/pix.
x 600 pix.
= 438. Å		0.73 Å/pix.
x 600 pix.
= 438. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.323
Minimum - Maximum-0.7038973 - 1.7127447
Average (Standard dev.)0.0053734835 (±0.05523259)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 438.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_56855_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56855_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-EM structure of yeast ribosome solved with EasyGrid

EntireName: Cryo-EM structure of yeast ribosome solved with EasyGrid
Components
  • Complex: Cryo-EM structure of yeast ribosome solved with EasyGrid

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Supramolecule #1: Cryo-EM structure of yeast ribosome solved with EasyGrid

SupramoleculeName: Cryo-EM structure of yeast ribosome solved with EasyGrid
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast)

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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: 7.4
Component:
ConcentrationFormulaName
20.0 mMHepesKOHHepesKOH
60.0 mMKClKCl
5.0 mMMg(OAc)2Mg(OAc)2
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
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

CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 135490
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: RELION (ver. 4)

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