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- EMDB-18911: 3DFlex refinement of wheat 40S ribosomal subunit cryo-EM reconstr... -

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Basic information

Entry
Database: EMDB / ID: EMD-18911
Title3DFlex refinement of wheat 40S ribosomal subunit cryo-EM reconstruction
Map data
Sample
  • Complex: Small ribosomal subunit from Triticum aestivum (common wheat)
Keywordssmall ribosomal subunit / wheat / eukaryotes / 40S / RIBOSOME
Biological speciesTriticum aestivum (bread wheat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsBaymukhametov TN / Kravchenko OV / Afonina ZA / Vasilenko KS
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Science Foundation19-74-20186 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2023
Title: High-Resolution Structure and Internal Mobility of a Plant 40S Ribosomal Subunit.
Authors: Olesya V Kravchenko / Timur N Baymukhametov / Zhanna A Afonina / Konstantin S Vassilenko /
Abstract: Ribosome is a major part of the protein synthesis machinery, and analysis of its structure is of paramount importance. However, the structure of ribosomes from only a limited number of organisms has ...Ribosome is a major part of the protein synthesis machinery, and analysis of its structure is of paramount importance. However, the structure of ribosomes from only a limited number of organisms has been resolved to date; it especially concerns plant ribosomes and ribosomal subunits. Here, we report a high-resolution cryo-electron microscopy reconstruction of the small subunit of the (common wheat) cytoplasmic ribosome. A detailed atomic model was built that includes the majority of the rRNA and some of the protein modifications. The analysis of the obtained data revealed structural peculiarities of the 40S subunit in the monocot plant ribosome. We applied the 3D Flexible Refinement approach to analyze the internal mobility of the 40S subunit and succeeded in decomposing it into four major motions, describing rotations of the head domain and a shift in the massive rRNA expansion segment. It was shown that these motions are almost uncorrelated and that the 40S subunit is flexible enough to spontaneously adopt any conformation it takes as a part of a translating ribosome or ribosomal complex. Here, we introduce the first high-resolution structure of an isolated plant 40S subunit and the first quantitative analysis of the flexibility of small ribosomal subunits, hoping that it will help in studying various aspects of ribosome functioning.
History
DepositionNov 16, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateJan 10, 2024-
Current statusJan 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18911.png

Downloads & links

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Map

FileDownload / File: emd_18911.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 440 pix.
= 413.6 Å		0.94 Å/pix.
x 440 pix.
= 413.6 Å		0.94 Å/pix.
x 440 pix.
= 413.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0017935634 - 2.1576426
Average (Standard dev.)0.0027168836 (±0.03952778)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 413.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18911_msk_1.map
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Half map: #1

Fileemd_18911_half_map_1.map
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Half map: #2

Fileemd_18911_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : Small ribosomal subunit from Triticum aestivum (common wheat)

EntireName: Small ribosomal subunit from Triticum aestivum (common wheat)
Components
  • Complex: Small ribosomal subunit from Triticum aestivum (common wheat)

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Supramolecule #1: Small ribosomal subunit from Triticum aestivum (common wheat)

SupramoleculeName: Small ribosomal subunit from Triticum aestivum (common wheat)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Triticum aestivum (bread wheat) / Strain: Moskovskaya / Organ: seed / Tissue: germ / 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: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
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: 0-32 / Number grids imaged: 1 / Number real images: 6201 / Average exposure time: 1.6 sec. / Average electron dose: 84.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.1 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 982063
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 256000
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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