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- EMDB-73574: Consensus map for Babesia divergens ribosome structure by single-... -

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Basic information

Entry
Database: EMDB / ID: EMD-73574
TitleConsensus map for Babesia divergens ribosome structure by single-particle cryo-EM (3D class1, A-, P-, and E-site tRNAs and mRNA)
Map dataphenix auto-sharpened map
Sample
  • Complex: 80S ribosome
    • Complex: 40S
    • Complex: 60S
KeywordstRNAs / RNA modification / 80S / RIBOSOME
Biological speciesBabesia divergens (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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: To Be Published
Title: Ribosomal architecture and rRNA modification landscape in the tick-borne parasite Babesia divergens
Authors: Gutierrez-Vargas C / Izhaki-Tavor LS / Calvopina-Chavez D / Keroack C / Copello P / Duraisingh M / Leger-Abraham M
History
DepositionOct 26, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73574.png

Downloads & links

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Map

FileDownload / File: emd_73574.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationphenix auto-sharpened 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: 3.5
Minimum - Maximum-6.2874346 - 16.328447000000001
Average (Standard dev.)0.000000000002717 (±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_73574_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_73574_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: #2

Fileemd_73574_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73574_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 reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.1 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, corresponding to the highest-resolution conformational class (3DC3, 80S with E-site tRNA) in this 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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