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- EMDB-17229: CRYO-EM CONSENSUS MAP OF LEISHMANIA MAJOR 80S RIBOSOME : PARENTAL... -

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Basic information

Entry
Database: EMDB / ID: EMD-17229
TitleCRYO-EM CONSENSUS MAP OF LEISHMANIA MAJOR 80S RIBOSOME : PARENTAL STRAIN
Map data80S_CONSENSUS_MAP
Sample
  • Complex: CRYO-EM MAPS OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE REPLICATE 1
KeywordsCRYO-EM / LEISHMANIA MAJOR / RIBOSOME / TRANSLATION
Biological speciesLeishmania major (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsRajan KS / Yonath A
Funding support Israel, European Union, 2 items
OrganizationGrant numberCountry
Israel Science Foundation Israel
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
DepositionApr 27, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17229.png

Downloads & links

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Map

FileDownload / File: emd_17229.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation80S_CONSENSUS_MAP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 480 pix.
= 408. Å		0.85 Å/pix.
x 480 pix.
= 408. Å		0.85 Å/pix.
x 480 pix.
= 408. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.02456834 - 0.0872087
Average (Standard dev.)-0.00043804903 (±0.003255824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: HALF MAP1 80S CONSENSUS MAP

Fileemd_17229_half_map_1.map
AnnotationHALF_MAP1_80S_CONSENSUS_MAP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HALF MAP2 80S CONSENSUS MAP

Fileemd_17229_half_map_2.map
AnnotationHALF_MAP2_80S_CONSENSUS_MAP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CRYO-EM MAPS OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE REPLICATE 1

EntireName: CRYO-EM MAPS OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE REPLICATE 1
Components
  • Complex: CRYO-EM MAPS OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE REPLICATE 1

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Supramolecule #1: CRYO-EM MAPS OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE REPLICATE 1

SupramoleculeName: CRYO-EM MAPS OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE REPLICATE 1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#85
Details: CRYO-EM MAPS OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE REPLICATE 1
Source (natural)Organism: Leishmania major (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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5t2a

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 212912
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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