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- EMDB-40769: Structure of the 48S translation initiation complex assembled on ... -

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Basic information

Entry
Database: EMDB / ID: EMD-40769
TitleStructure of the 48S translation initiation complex assembled on the encephalomyocarditis virus IRES.
Map data40S-head focused
Sample
  • Complex: EMCV IRES 40SIC
    • Complex: 40SIC
    • Complex: EMCV IRES
KeywordsEMCV / IRES / Cryo-EM / 40SIC / RIBOSOME
Biological speciesOryctolagus cuniculus (rabbit) / Encephalomyocarditis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBhattacharjee S / Abaeva IS / Brown ZP / Arhab Y / Fallah H / Jeevan GC / Hellen CUT / Frank J / Pestova TV
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM139453 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM29169 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM122602 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM097014 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI123406 United States
CitationJournal: To Be Published
Title: Structure of the 48S translation initiation complex assembled on the encephalomyocarditis virus IRES.
Authors: Bhattacharjee S / Abaeva IS / Brown ZP / Arhab Y / Fallah H / Jeevan GC / Hellen CUT / Frank J / Pestova TV
History
DepositionMay 12, 2023-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateAug 28, 2024-
Current statusAug 28, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40769.png

Downloads & links

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Map

FileDownload / File: emd_40769.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation40S-head focused
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 320 pix.
= 396.8 Å		1.24 Å/pix.
x 320 pix.
= 396.8 Å		1.24 Å/pix.
x 320 pix.
= 396.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.381
Minimum - Maximum-1.783411 - 2.5930917
Average (Standard dev.)0.003237638 (±0.053555034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 396.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40769_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 40S-head focused half1

Fileemd_40769_half_map_1.map
Annotation40S-head focused half1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 40S-head focused half2

Fileemd_40769_half_map_2.map
Annotation40S-head focused half2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : EMCV IRES 40SIC

EntireName: EMCV IRES 40SIC
Components
  • Complex: EMCV IRES 40SIC
    • Complex: 40SIC
    • Complex: EMCV IRES

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Supramolecule #1: EMCV IRES 40SIC

SupramoleculeName: EMCV IRES 40SIC / type: complex / ID: 1 / Parent: 0 / Details: Cryo_EM

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Supramolecule #2: 40SIC

SupramoleculeName: 40SIC / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Supramolecule #3: EMCV IRES

SupramoleculeName: EMCV IRES / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Encephalomyocarditis virus

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 262752
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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