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- EMDB-14051: Specific features and methylation sites of a plant ribosome. 80S ... -

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Basic information

Entry
Database: EMDB / ID: EMD-14051
TitleSpecific features and methylation sites of a plant ribosome. 80S translating ribosome (A/A-P/P-E/E).
Map data
Sample
  • Complex: 80S translating ribosome (A/A-P/P-E/E)
KeywordsSolanum lycopersicum / cytosolic ribosome / 80S / plant / rRNA / RIBOSOME
Biological speciesSolanum lycopersicum (tomato)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsCottilli P / Itoh Y / Amunts A
Funding supportEuropean Union, 4 items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107European Union
European Research Council (ERC)ERC-2018-StG-805230European Union
Knut and Alice Wallenberg Foundation2018.0080European Union
European Molecular Biology Organization (EMBO)H2020-MSCA-IF-2017European Union
CitationJournal: Plant Commun / Year: 2022
Title: Cryo-EM structure and rRNA modification sites of a plant ribosome.
Authors: Patrick Cottilli / Yuzuru Itoh / Yuko Nobe / Anton S Petrov / Purificación Lisón / Masato Taoka / Alexey Amunts /
Abstract: Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to ...Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to changing environmental cues via the deposition of chemical modifications into rRNA. Here, we present the structure of a plant ribosome from tomato and a quantitative mass spectrometry analysis of its rRNAs. The study reveals fine features of the ribosomal proteins and 71 plant-specific rRNA modifications, and it re-annotates 30 rRNA residues in the available sequence. At the protein level, isoAsp is found in position 137 of uS11, and a zinc finger previously believed to be universal is missing from eL34, suggesting a lower effect of zinc deficiency on protein synthesis in plants. At the rRNA level, the plant ribosome differs markedly from its human counterpart with respect to the spatial distribution of modifications. Thus, it represents an additional layer of gene expression regulation, highlighting the molecular signature of a plant ribosome. The results provide a reference model of a plant ribosome for structural studies and an accurate marker for molecular ecology.
History
DepositionDec 19, 2021-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14051.png

Downloads & links

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Map

FileDownload / File: emd_14051.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 540 pix.
= 448.2 Å		0.83 Å/pix.
x 540 pix.
= 448.2 Å		0.83 Å/pix.
x 540 pix.
= 448.2 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.21099427 - 0.41769642
Average (Standard dev.)0.000055045784 (±0.00939942)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 448.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14051_msk_1.map
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Half map: #1

Fileemd_14051_half_map_1.map
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Half map: #2

Fileemd_14051_half_map_2.map
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Sample components

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Entire : 80S translating ribosome (A/A-P/P-E/E)

EntireName: 80S translating ribosome (A/A-P/P-E/E)
Components
  • Complex: 80S translating ribosome (A/A-P/P-E/E)

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Supramolecule #1: 80S translating ribosome (A/A-P/P-E/E)

SupramoleculeName: 80S translating ribosome (A/A-P/P-E/E) / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Solanum lycopersicum (tomato)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

3883

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36183
FSC plot (resolution estimation)

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