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- EMDB-40771: Structure of the 48S translation initiation complex assembled on ... -

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Basic information

Entry
Database: EMDB / ID: EMD-40771
TitleStructure of the 48S translation initiation complex assembled on the encephalomyocarditis virus IRES
Map dataeIF3-40Spart-map
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: 3.3 Å
AuthorsBhattacharjee S / Abaeva IS / Brown ZP / Arhab Y / Fallah H / Jeevan JC / 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)R35 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: EMBO J / Year: 2026
Title: The mechanism of ribosomal recruitment during translation initiation on the Type 2 encephalomyocarditis virus IRES.
Authors: Sayan Bhattacharjee / Irina S Abaeva / Zuben P Brown / Yani Arhab / Hengameh Fallah / Christopher U T Hellen / Joachim Frank / Tatyana V Pestova /
Abstract: The encephalomyocarditis virus (EMCV) internal ribosomal entry side (IRES) and other Type 2 IRESs favor translation of the viral genome during infection. The domains H-L of these IRESs specifically ...The encephalomyocarditis virus (EMCV) internal ribosomal entry side (IRES) and other Type 2 IRESs favor translation of the viral genome during infection. The domains H-L of these IRESs specifically interact with the cellular translation initiation factors eIF4G/eIF4A through their essential JK domain. However, the JK domain is not sufficient for IRES activity, which also strictly requires the preceding domain I of unknown function. To identify interactions that drive ribosomal attachment to eIF4G/eIF4A-bound Type 2 IRESs, we determined the cryo-EM structure of 48S initiation complexes formed on the EMCV IRES. The apical cloverleaf of domain I contacts ribosomal proteins uS13 and uS19 via its subdomain Id, whereas the essential GNRA tetraloop in subdomain Ic interacts with the TψC domain of initiator tRNA. The IRES-tRNA interaction also provides a mechanism for release of the IRES after eIF2 is replaced by eIF5B during subunit joining to allow attachment of 60S subunits. Functional assays supported the exceptional role of these interactions for initiation on this IRES. The strong conservation of the apex of domain I amongst Type 2 IRESs suggests that the reported interactions provide a common general mechanism of ribosomal attachment on them all.
History
DepositionMay 12, 2023-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40771.png

Downloads & links

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Map

FileDownload / File: emd_40771.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationeIF3-40Spart-map
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: 0.139
Minimum - Maximum-1.0879776 - 2.3011677
Average (Standard dev.)0.001194856 (±0.0420118)
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_40771_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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Half map: eIF3-40Spart-half1

Fileemd_40771_half_map_1.map
AnnotationeIF3-40Spart-half1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: eIF3-40Spart-half2

Fileemd_40771_half_map_2.map
AnnotationeIF3-40Spart-half2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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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

CTF correctionSoftware - Name: RELION (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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