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- EMDB-36334: Atomic structure of wheat ribosome reveals unique features of the... -

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Basic information

Entry
Database: EMDB / ID: EMD-36334
TitleAtomic structure of wheat ribosome reveals unique features of the plant ribosomes
Map data
Sample
  • Complex: The large subunit of wheat Ribosome
KeywordsProtein Synthesis Machinery / Eukaryotic Ribosome / Plant / TRANSLATION / RIBOSOME
Biological speciesTriticum aestivum (bread wheat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsMishra RK / Sharma PN / Hussain T
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Citation
Journal: Structure / Year: 2024
Title: Cryo-EM structure of wheat ribosome reveals unique features of the plant ribosomes.
Authors: Rishi Kumar Mishra / Prafful Sharma / Faisal Tarique Khaja / Adwaith B Uday / Tanweer Hussain /
Abstract: Plants being sessile organisms exhibit unique features in ribosomes, which might aid in rapid gene expression and regulation in response to varying environmental conditions. Here, we present high- ...Plants being sessile organisms exhibit unique features in ribosomes, which might aid in rapid gene expression and regulation in response to varying environmental conditions. Here, we present high-resolution structures of the 60S and 80S ribosomes from wheat, a monocot staple crop plant (Triticum aestivum). While plant ribosomes have unique plant-specific rRNA modification (Cm1847) in the peptide exit tunnel (PET), the zinc-finger motif in eL34 is absent, and uL4 is extended, making an exclusive interaction network. We note differences in the eL15-helix 11 (25S) interaction, eL6-ES7 assembly, and certain rRNA chemical modifications between monocot and dicot ribosomes. In eukaryotes, we observe highly conserved rRNA modification (Gm75) in 5.8S rRNA and a flipped base (G1506) in PET. These features are likely involved in sensing or stabilizing nascent chain. Finally, we discuss the importance of the universal conservation of three consecutive rRNA modifications in all ribosomes for their interaction with A-site aminoacyl-tRNA.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Uday AB / Khaja FT
History
DepositionMay 28, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36334.png

Downloads & links

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Map

FileDownload / File: emd_36334.map.gz / Format: CCP4 / Size: 282.6 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.)
1.07 Å/pix.
x 420 pix.
= 449.4 Å		1.07 Å/pix.
x 420 pix.
= 449.4 Å		1.07 Å/pix.
x 420 pix.
= 449.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-3.3855853 - 7.2507463
Average (Standard dev.)0.0056640473 (±0.2524563)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 449.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36334_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_36334_half_map_2.map
Projections & Slices
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Sample components

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Entire : The large subunit of wheat Ribosome

EntireName: The large subunit of wheat Ribosome
Components
  • Complex: The large subunit of wheat Ribosome

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Supramolecule #1: The large subunit of wheat Ribosome

SupramoleculeName: The large subunit of wheat Ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#44
Source (natural)Organism: Triticum aestivum (bread wheat)

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample is the large subunit of wheat ribosome

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 44.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 2.7 µm / Calibrated magnification: 75000 / Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4v7e

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 105563
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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