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- EMDB-55223: CRYO-EM FOCUSED REFINEMENT MAP OF TRYPANOSOMA BRUCEI BLOODSTREAM ... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-55223
TitleCRYO-EM FOCUSED REFINEMENT MAP OF TRYPANOSOMA BRUCEI BLOODSTREAM FORM 80S RIBOSOME
Map dataBody 1 of the composite map
Sample
  • Complex: CRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI BLOODSTREAM FORM 80S RIBOSOME
KeywordsCRYO-EM / TRYPANOSOMA BRUCEI / BLOODSTREAM FORM / 80S / RIBOSOME
Biological speciesTrypanosoma brucei brucei (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsRajan KS / Yonath A
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation Israel
CitationJournal: To Be Published
Title: CRYO-EM FOCUSED REFINEMENT MAP OF TRYPANOSOMA BRUCEI BLOODSTREAM FORM 80S RIBOSOME
Authors: Rajan KS / Yonath A
History
DepositionSep 29, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55223.png

Downloads & links

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Map

FileDownload / File: emd_55223.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBody 1 of the composite map
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-0.026201608 - 0.06755296
Average (Standard dev.)-0.00027342298 (±0.0024699736)
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: Body 2 of the composite map

Fileemd_55223_additional_1.map
AnnotationBody 2 of the composite map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Body 3 of the composite map

Fileemd_55223_additional_2.map
AnnotationBody 3 of the composite map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Halfmap of Body 2

Fileemd_55223_additional_3.map
AnnotationHalfmap of Body 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Halfmap of Body 3

Fileemd_55223_additional_4.map
AnnotationHalfmap of Body 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Halfmap of Body 2

Fileemd_55223_additional_5.map
AnnotationHalfmap of Body 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Halfmap of Body 3

Fileemd_55223_additional_6.map
AnnotationHalfmap of Body 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap of Body 1

Fileemd_55223_half_map_1.map
AnnotationHalfmap of Body 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap of Body 1

Fileemd_55223_half_map_2.map
AnnotationHalfmap 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 : CRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI BLOODSTREAM FORM 80S RIBOSOME

EntireName: CRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI BLOODSTREAM FORM 80S RIBOSOME
Components
  • Complex: CRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI BLOODSTREAM FORM 80S RIBOSOME

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Supramolecule #1: CRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI BLOODSTREAM FORM 80S RIBOSOME

SupramoleculeName: CRYO-EM STRUCTURE OF TRYPANOSOMA BRUCEI BLOODSTREAM FORM 80S RIBOSOME
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#86
Source (natural)Organism: Trypanosoma brucei brucei (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
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.05 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

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

8ova

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 570752
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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