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- EMDB-73577: Multi-body SSU body map for Babesia divergens ribosome structure ... -

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Basic information

Entry
Database: EMDB / ID: EMD-73577
TitleMulti-body SSU body map for Babesia divergens ribosome structure by single-particle cryo-EM (3D class1, A-, P-, and E-site tRNAs and mRNA)
Map dataphenix auto-sharpen map
Sample
  • Complex: 80S ribosome
    • Complex: 40S
    • Complex: 60S
KeywordstRNAs / RNA modification / 80S / RIBOSOME
Biological speciesBabesia divergens (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsGutierrez-Vargas C / Leger-Abraham M
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R21AI178196-02 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI007061 United States
CitationJournal: bioRxiv / Year: 2025
Title: Ribosomal Architecture and rRNA Modification Landscape in the Tick-Borne Parasite .
Authors: Cristina Gutierrez-Vargas / Lee S Izhaki-Tavor / Diana Calvopina-Chavez / Caroline D Keroack / Pablo Copello / Manoj T Duraisingh / Mélissa Léger-Abraham /
Abstract: is a tick-borne intracellular apicomplexan parasite responsible for diseases ranging from mild to fatal, with a broadening geographic distribution. Due to the complex life cycle of species, their ... is a tick-borne intracellular apicomplexan parasite responsible for diseases ranging from mild to fatal, with a broadening geographic distribution. Due to the complex life cycle of species, their survival depends on the precise control of gene expression, which is primarily regulated by epigenetic, transcriptional, and post-transcriptional mechanisms. High-resolution structural information on key components of the translation machinery, such as ribosomes, could aid in the development of antiparasitic drugs. Here, we report cryo-EM ribosome structures (2.6 Å) from the tick-borne apicomplexan pathogen , showing associated tRNAs, an mRNA fragment, and RACK1, a signaling scaffold crucial to translation regulation. Density map analysis displays ribosome regions at atomic resolution (1.7 Å), which, when combined with nanopore sequencing, enabled the comprehensive identification of rRNA modifications, including modifications unreported in other organisms. The new rRNA modifications localize not only to the reduced rRNA expansion segments but also to functionally essential ribosomal sites, uncovering new avenues for therapeutic intervention against babesiosis.
History
DepositionOct 26, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73577.png

Downloads & links

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Map

FileDownload / File: emd_73577.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationphenix auto-sharpen map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 448 pix.
= 369.6 Å		0.83 Å/pix.
x 448 pix.
= 369.6 Å		0.83 Å/pix.
x 448 pix.
= 369.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-8.920144000000001 - 22.80048
Average (Standard dev.)0.000000000001188 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 369.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73577_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: relion postprocess map

Fileemd_73577_additional_1.map
Annotationrelion postprocess map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73577_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_73577_half_map_2.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 : 80S ribosome

EntireName: 80S ribosome
Components
  • Complex: 80S ribosome
    • Complex: 40S
    • Complex: 60S

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Supramolecule #1: 80S ribosome

SupramoleculeName: 80S ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#78
Source (natural)Organism: Babesia divergens (eukaryote) / Strain: Rouen 1987

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Supramolecule #2: 40S

SupramoleculeName: 40S / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #42-#72, #74-#75, #78
Source (natural)Organism: Babesia divergens (eukaryote) / Strain: Rouen 1987

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Supramolecule #3: 60S

SupramoleculeName: 60S / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#41, #73, #76-#77
Source (natural)Organism: Babesia divergens (eukaryote) / Strain: Rouen 1987

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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: 7.4
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMKCH3COOPotassium acetate
10.0 mMNH4CH3COOAmmonium acetate
10.0 mMMg(CH3COO)2Magnesium acetate
5.0 mMHSCH2CH2OH2-Mercaptoethanol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.037 kPa
Details: The grid had an additional ultrathin carbon continuous layer (2 nm)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: SerialEM (ver. 3.8.6)
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 12144 / Average exposure time: 1.4 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
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: 1259788
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.13) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 50001) / Number images used: 26467
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. version 30001)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetailsPDB ID
source_name: Other, initial_model_type: in silico modelribosomal proteins
chain_id: L3, source_name: PDB, initial_model_type: experimental model5S

9ygm

chain_id: L4, source_name: PDB, initial_model_type: experimental model5.8S

9ygm

chain_id: L5, source_name: PDB, initial_model_type: experimental model28S rRNA

9ygm

chain_id: S1, source_name: PDB, initial_model_type: experimental model18S rRNA

9ygm

SoftwareName: UCSF ChimeraX
DetailsProtein chains were built de novo with ModelAngelo. The rRNA chains from PDB 9YGM, which corresponds to the highest-resolution conformational class (3DC3, 80S with E-site tRNA) from the same dataset, were rigid-body fit and remodeled. The complete model then underwent iterative rounds of manual adjustment in Coot and real-space refinement in Phenix.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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