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- EMDB-47230: Focused map for the 60S subunit of the hypomthylated yeast 80S fr... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-47230
TitleFocused map for the 60S subunit of the hypomthylated yeast 80S from nutrient-limiting cells bound with Suppressor of ToM1 (Stm1)
Map data
Sample
  • Complex: Hypomthylated yeast 80S from nutrient-limiting cells bound with Suppressor of ToM1 (Stm1)
KeywordsRNA modification / ribosome maturation / translation regulation / RIBOSOME
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhao Y / Li H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124622 United States
CitationJournal: to be published
Title: Regulation of Translation by Ribosome RNA 2'-O-Methylation
Authors: Zhao Y / Li H
History
DepositionOct 8, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47230.png

Downloads & links

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Map

FileDownload / File: emd_47230.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-7.192603 - 11.247066999999999
Average (Standard dev.)0.03344895 (±0.350786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_47230_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_47230_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 : Hypomthylated yeast 80S from nutrient-limiting cells bound with S...

EntireName: Hypomthylated yeast 80S from nutrient-limiting cells bound with Suppressor of ToM1 (Stm1)
Components
  • Complex: Hypomthylated yeast 80S from nutrient-limiting cells bound with Suppressor of ToM1 (Stm1)

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Supramolecule #1: Hypomthylated yeast 80S from nutrient-limiting cells bound with S...

SupramoleculeName: Hypomthylated yeast 80S from nutrient-limiting cells bound with Suppressor of ToM1 (Stm1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#78, #80-#82
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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: 7.5
Sugar embeddingMaterial: carbon
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7mpi

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 373415
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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