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- EMDB-18515: CRYO-EM FOCUSED REFINED MAP OF LEISHMANIA MAJOR 80S RIBOSOME : LM... -

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Basic information

Entry
Database: EMDB / ID: EMD-18515
TitleCRYO-EM FOCUSED REFINED MAP OF LEISHMANIA MAJOR 80S RIBOSOME : LM32Cs1C1 Mutant snoRNA overexpression class 4
Map data60S focused refined map
Sample
  • Complex: CRYO-EM FOCUSED REFINED MAP OF LEISHMANIA MAJOR 80S RIBOSOME : LM32Cs1C1 Mutant snoRNA overexpression class 4
KeywordsLeishmania major / snoRNA / Ribosome
Biological speciesLeishmania major strain Friedlin (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.43 Å
AuthorsRajan KS / Yonath A / Bashan A
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: CRYO-EM FOCUSED REFINED MAP OF LEISHMANIA MAJOR 80S RIBOSOME : LM32Cs1C1 Mutant snoRNA overexpression class 4
Authors: Rajan KS / Yonath A / Bashan A
History
DepositionSep 27, 2023-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18515.png

Downloads & links

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Map

FileDownload / File: emd_18515.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation60S focused refined 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: 0.01
Minimum - Maximum-0.0148908645 - 0.06555758
Average (Standard dev.)-0.00021928479 (±0.0026730474)
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: 40S head focused refined map

Fileemd_18515_additional_1.map
Annotation40S head focused refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 40S body focused refined map

Fileemd_18515_additional_2.map
Annotation40S body focused refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 for 60S focused refined map

Fileemd_18515_half_map_1.map
AnnotationHalf map 1 for 60S focused refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 for 60S focused refined map

Fileemd_18515_half_map_2.map
AnnotationHalf map 2 for 60S focused refined 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 FOCUSED REFINED MAP OF LEISHMANIA MAJOR 80S RIBOSOME : LM...

EntireName: CRYO-EM FOCUSED REFINED MAP OF LEISHMANIA MAJOR 80S RIBOSOME : LM32Cs1C1 Mutant snoRNA overexpression class 4
Components
  • Complex: CRYO-EM FOCUSED REFINED MAP OF LEISHMANIA MAJOR 80S RIBOSOME : LM32Cs1C1 Mutant snoRNA overexpression class 4

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Supramolecule #1: CRYO-EM FOCUSED REFINED MAP OF LEISHMANIA MAJOR 80S RIBOSOME : LM...

SupramoleculeName: CRYO-EM FOCUSED REFINED MAP OF LEISHMANIA MAJOR 80S RIBOSOME : LM32Cs1C1 Mutant snoRNA overexpression class 4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#86
Details: CRYO-EM FOCUSED REFINED MAP OF LEISHMANIA MAJOR 80S RIBOSOME : LM32Cs1C1 Mutant snoRNA overexpression class 4
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
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
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: 0.94 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.3 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: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 178107
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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