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- EMDB-15018: Translating 80S ribosome from HeLa cell lysate -

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Basic information

Entry
Database: EMDB / ID: EMD-15018
TitleTranslating 80S ribosome from HeLa cell lysate
Map data
Sample
  • Complex: Polyribosomes from HeLa cytoplasm
Keywordseukaryotic polyribosome ribosomal translation complex / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsBaymukhametov TN / Chesnokov YM / Afonina ZA
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Science Foundation19-74-20186 Russian Federation
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Polyribosomes of circular topology are prevalent in mammalian cells.
Authors: Timur N Baymukhametov / Dmitry N Lyabin / Yury M Chesnokov / Ivan I Sorokin / Evgeniya V Pechnikova / Alexander L Vasiliev / Zhanna A Afonina /
Abstract: Polyribosomes, the groups of ribosomes simultaneously translating a single mRNA molecule, are very common in both, prokaryotic and eukaryotic cells. Even in early EM studies, polyribosomes have been ...Polyribosomes, the groups of ribosomes simultaneously translating a single mRNA molecule, are very common in both, prokaryotic and eukaryotic cells. Even in early EM studies, polyribosomes have been shown to possess various spatial conformations, including a ring-shaped configuration which was considered to be functionally important. However, a recent in situ cryo-ET analysis of predominant regular inter-ribosome contacts did not confirm the abundance of ring-shaped polyribosomes in a cell cytoplasm. To address this discrepancy, here we analyzed the cryo-ET structure of polyribosomes in diluted lysates of HeLa cells. It was shown that the vast majority of the ribosomes were combined into polysomes and were proven to be translationally active. Tomogram analysis revealed that circular polyribosomes are indeed very common in the cytoplasm, but they mostly possess pseudo-regular structures without specific inter-ribosomal contacts. Although the size of polyribosomes varied widely, most circular polysomes were relatively small in size (4-8 ribosomes). Our results confirm the recent data that it is cellular mRNAs with short ORF that most commonly form circular structures providing an enhancement of translation.
History
DepositionMay 23, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15018.png

Downloads & links

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Map

FileDownload / File: emd_15018.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
3.7 Å/pix.
x 128 pix.
= 473.6 Å		3.7 Å/pix.
x 128 pix.
= 473.6 Å		3.7 Å/pix.
x 128 pix.
= 473.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.7
Minimum - Maximum-0.7803904 - 5.390079
Average (Standard dev.)0.16090147 (±0.61646783)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 473.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15018_msk_1.map
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Half map: #1

Fileemd_15018_half_map_1.map
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Half map: #2

Fileemd_15018_half_map_2.map
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Sample components

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Entire : Polyribosomes from HeLa cytoplasm

EntireName: Polyribosomes from HeLa cytoplasm
Components
  • Complex: Polyribosomes from HeLa cytoplasm

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Supramolecule #1: Polyribosomes from HeLa cytoplasm

SupramoleculeName: Polyribosomes from HeLa cytoplasm / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Polysomes in cell lysate obtained by osmotic lysis of HeLa cells
Source (natural)Organism: Homo sapiens (human) / Strain: HeLa / Location in cell: cytoplasm

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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: 7.6
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 26.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 3783 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 18000
Specialist opticsSpherical aberration corrector: Cs image corrector (CEOS, Germany)
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-24 / Number grids imaged: 1 / Number real images: 500 / Average electron dose: 61.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 93249
Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 10996
FSC plot (resolution estimation)

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