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- EMDB-17165: CRYO-EM FOCUSED REFINEMENT MAPS OF LEISHMANIA MAJOR 80S RIBOSOME ... -

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Basic information

Entry
Database: EMDB / ID: EMD-17165
TitleCRYO-EM FOCUSED REFINEMENT MAPS OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE REPLICATE 1
Map dataFocused refinement Body 1
Sample
  • Complex: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE
KeywordsCRYO-EM LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE / RIBOSOME
Biological speciesLeishmania major strain Friedlin (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsRajan KS / Yonath A / Bashan A
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation Israel
CitationJournal: To Be Published
Title: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE
Authors: Rajan KS
History
DepositionApr 20, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17165.png

Downloads & links

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Map

FileDownload / File: emd_17165.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refinement Body 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 440 pix.
= 374. Å		0.85 Å/pix.
x 440 pix.
= 374. Å		0.85 Å/pix.
x 440 pix.
= 374. 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-0.029944103 - 0.07551904
Average (Standard dev.)-0.00019081937 (±0.0029305532)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 374.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Focused refinement Body 3

Fileemd_17165_additional_1.map
AnnotationFocused refinement Body 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused refinement Body 2

Fileemd_17165_additional_2.map
AnnotationFocused refinement Body 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 for Focused refinement Body 1

Fileemd_17165_half_map_1.map
AnnotationHalf map 2 for Focused refinement Body 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 for Focused refinement Body 1

Fileemd_17165_half_map_2.map
AnnotationHalf map 1 for Focused refinement 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 LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE

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

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

SupramoleculeName: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#82
Details: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE
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
Component:
ConcentrationName
20.0 mMHEPES
100.0 mMKOAc
10.0 mMMg(OAc)2
10.0 mMNH4OAc
1.0 mMDTT
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5t2a

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 742580
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial model
PDB IDChain

6az1

source_name: PDB, initial_model_type: experimental model

6az3

source_name: PDB, initial_model_type: experimental model

5t2a

source_name: PDB, initial_model_type: experimental model

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