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- EMDB-19676: CRYO-EM FOCUSED REFINEMENT MAP OF LEISHMANIA MAJOR 80S RIBOSOME W... -

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Basic information

Entry
Database: EMDB / ID: EMD-19676
TitleCRYO-EM FOCUSED REFINEMENT MAP OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-site tRNA AND mRNA : LM32Cs3H1 sKO STRAIN
Map dataBody1 of focused refinement
Sample
  • Complex: 80S RIBOSOME WITH A/P/E-site tRNA AND mRNA
KeywordsCRYO-EM / LEISHMANIA MAJOR / 80S / RIBOSOME
Biological speciesLeishmania major strain Friedlin (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsRajan KS / Yonath A
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Cell Rep / Year: 2024
Title: Structural and mechanistic insights into the function of Leishmania ribosome lacking a single pseudouridine modification.
Authors: K Shanmugha Rajan / Saurav Aryal / Disha-Gajanan Hiregange / Anat Bashan / Hava Madmoni / Mika Olami / Tirza Doniger / Smadar Cohen-Chalamish / Pascal Pescher / Masato Taoka / Yuko Nobe / ...Authors: K Shanmugha Rajan / Saurav Aryal / Disha-Gajanan Hiregange / Anat Bashan / Hava Madmoni / Mika Olami / Tirza Doniger / Smadar Cohen-Chalamish / Pascal Pescher / Masato Taoka / Yuko Nobe / Aliza Fedorenko / Tanaya Bose / Ella Zimermann / Eric Prina / Noa Aharon-Hefetz / Yitzhak Pilpel / Toshiaki Isobe / Ron Unger / Gerald F Späth / Ada Yonath / Shulamit Michaeli /
Abstract: Leishmania is the causative agent of cutaneous and visceral diseases affecting millions of individuals worldwide. Pseudouridine (Ψ), the most abundant modification on rRNA, changes during the ...Leishmania is the causative agent of cutaneous and visceral diseases affecting millions of individuals worldwide. Pseudouridine (Ψ), the most abundant modification on rRNA, changes during the parasite life cycle. Alterations in the level of a specific Ψ in helix 69 (H69) affected ribosome function. To decipher the molecular mechanism of this phenotype, we determine the structure of ribosomes lacking the single Ψ and its parental strain at ∼2.4-3 Å resolution using cryo-EM. Our findings demonstrate the significance of a single Ψ on H69 to its structure and the importance for its interactions with helix 44 and specific tRNAs. Our study suggests that rRNA modification affects translation of mRNAs carrying codon bias due to selective accommodation of tRNAs by the ribosome. Based on the high-resolution structures, we propose a mechanism explaining how the ribosome selects specific tRNAs.
History
DepositionFeb 17, 2024-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19676.png

Downloads & links

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Map

FileDownload / File: emd_19676.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBody1 of focused refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 480 pix.
= 380.64 Å		0.79 Å/pix.
x 480 pix.
= 380.64 Å		0.79 Å/pix.
x 480 pix.
= 380.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.793 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.015098529 - 0.038448676
Average (Standard dev.)-0.00019400488 (±0.001841112)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 380.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Body2 of focused refinement

Fileemd_19676_additional_1.map
AnnotationBody2 of focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Body3 of focused refinement

Fileemd_19676_additional_2.map
AnnotationBody3 of focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map1 of body 1

Fileemd_19676_half_map_1.map
AnnotationHalf map1 of body 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map1 of body 1

Fileemd_19676_half_map_2.map
AnnotationHalf map1 of body 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 80S RIBOSOME WITH A/P/E-site tRNA AND mRNA

EntireName: 80S RIBOSOME WITH A/P/E-site tRNA AND mRNA
Components
  • Complex: 80S RIBOSOME WITH A/P/E-site tRNA AND mRNA

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Supramolecule #1: 80S RIBOSOME WITH A/P/E-site tRNA AND mRNA

SupramoleculeName: 80S RIBOSOME WITH A/P/E-site tRNA AND mRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#89
Details: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-site tRNA AND mRNA : LM32Cs3H1 sKO STRAIN
Source (natural)Organism: Leishmania major strain Friedlin (eukaryote)

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 1.273 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

17216

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 490938
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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