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- EMDB-47259: Focused refined density of the head domain of the 40S domain of h... -

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Basic information

Entry
Database: EMDB / ID: EMD-47259
TitleFocused refined density of the head domain of the 40S domain of hypomethylated ribosome isolated from nutrient-limiting yeast incubated with hygromycin B
Map data
Sample
  • Complex: Hypomethylated ribosome isolated from nutrient-limiting yeast cells incubated with hygromycin B
KeywordsRNA modification / 2'-O-methylation / IRES initiation / eEF2 / Ribosome
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.96 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 9, 2024-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47259.png

Downloads & links

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Map

FileDownload / File: emd_47259.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: 0.5
Minimum - Maximum-1.2801478 - 3.3302977
Average (Standard dev.)0.008776802 (±0.06568222)
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: #1

Fileemd_47259_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_47259_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 : Hypomethylated ribosome isolated from nutrient-limiting yeast cel...

EntireName: Hypomethylated ribosome isolated from nutrient-limiting yeast cells incubated with hygromycin B
Components
  • Complex: Hypomethylated ribosome isolated from nutrient-limiting yeast cells incubated with hygromycin B

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Supramolecule #1: Hypomethylated ribosome isolated from nutrient-limiting yeast cel...

SupramoleculeName: Hypomethylated ribosome isolated from nutrient-limiting yeast cells incubated with hygromycin B
type: complex / ID: 1 / Parent: 0
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

MicroscopeTFS 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:

7mpj

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 160722
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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