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- EMDB-16740: Human 80S ribosome with ES27L at conformation 3 in untreated cells -

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Basic information

Entry
Database: EMDB / ID: EMD-16740
TitleHuman 80S ribosome with ES27L at conformation 3 in untreated cells
Map data
Sample
  • Complex: Human 80S ribosome with ES27L at conformation 3 in untreated cells
Keywordshuman / 80S ribosome / translation / tRNA / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 6.9 Å
AuthorsXing H / Welsch S / Turonova B / Beck M
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Science / Year: 2023
Title: Translation dynamics in human cells visualized at high resolution reveal cancer drug action.
Authors: Huaipeng Xing / Reiya Taniguchi / Iskander Khusainov / Jan Philipp Kreysing / Sonja Welsch / Beata Turoňová / Martin Beck /
Abstract: Ribosomes catalyze protein synthesis by cycling through various functional states. These states have been extensively characterized in vitro, but their distribution in actively translating human ...Ribosomes catalyze protein synthesis by cycling through various functional states. These states have been extensively characterized in vitro, but their distribution in actively translating human cells remains elusive. We used a cryo-electron tomography-based approach and resolved ribosome structures inside human cells with high resolution. These structures revealed the distribution of functional states of the elongation cycle, a Z transfer RNA binding site, and the dynamics of ribosome expansion segments. Ribosome structures from cells treated with Homoharringtonine, a drug used against chronic myeloid leukemia, revealed how translation dynamics were altered in situ and resolve the small molecules within the active site of the ribosome. Thus, structural dynamics and drug effects can be assessed at high resolution within human cells.
History
DepositionFeb 20, 2023-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateJul 19, 2023-
Current statusJul 19, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16740.png

Downloads & links

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Map

FileDownload / File: emd_16740.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 320 pix.
= 380.16 Å		1.19 Å/pix.
x 320 pix.
= 380.16 Å		1.19 Å/pix.
x 320 pix.
= 380.16 Å

Surface

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.188 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.004661224 - 0.014349414
Average (Standard dev.)0.00032228758 (±0.0014998175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin172172172
Dimensions320320320
Spacing320320320
CellA=B=C: 380.15997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_16740_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16740_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human 80S ribosome with ES27L at conformation 3 in untreated cells

EntireName: Human 80S ribosome with ES27L at conformation 3 in untreated cells
Components
  • Complex: Human 80S ribosome with ES27L at conformation 3 in untreated cells

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Supramolecule #1: Human 80S ribosome with ES27L at conformation 3 in untreated cells

SupramoleculeName: Human 80S ribosome with ES27L at conformation 3 in untreated cells
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.46 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.5 µm
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: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 4715
ExtractionNumber tomograms: 358 / Number images used: 286400
Final angle assignmentType: OTHER

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