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- EMDB-51217: Structure of Edeine-30S-IF1-IF3-mRNA-tRNA translation pre-initiat... -

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Basic information

Entry
Database: EMDB / ID: EMD-51217
TitleStructure of Edeine-30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex, open form
Map data
Sample
  • Complex: Structure of Edeine-30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex, open form
KeywordsRibosome / Antibiotic / TRANSLATION
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSafdari HA / Wilson DN
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2025
Title: The translation inhibitors kasugamycin, edeine and GE81112 target distinct steps during 30S initiation complex formation.
Authors: Haaris A Safdari / Martino Morici / Ana Sanchez-Castro / Andrea Dallapè / Helge Paternoga / Anna Maria Giuliodori / Attilio Fabbretti / Pohl Milón / Daniel N Wilson /
Abstract: During bacterial translation initiation, the 30S ribosomal subunit, initiation factors, and initiator tRNA define the reading frame of the mRNA. This process is inhibited by kasugamycin, edeine and ...During bacterial translation initiation, the 30S ribosomal subunit, initiation factors, and initiator tRNA define the reading frame of the mRNA. This process is inhibited by kasugamycin, edeine and GE81112, however, their mechanisms of action have not been fully elucidated. Here we present cryo-electron microscopy structures of 30S initiation intermediate complexes formed in the presence of kasugamycin, edeine and GE81112 at resolutions of 2.0-2.9 Å. The structures reveal that all three antibiotics bind within the E-site of the 30S and preclude 30S initiation complex formation. While kasugamycin and edeine affect early steps of 30S pre-initiation complex formation, GE81112 stalls pre-initiation complex formation at a further step by allowing start codon recognition, but impeding IF3 departure. Collectively, our work highlights how chemically distinct compounds binding at a conserved site on the 30S can interfere with translation initiation in a unique manner.
History
DepositionJul 30, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51217.png

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Map

FileDownload / File: emd_51217.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332.8 Å		0.83 Å/pix.
x 400 pix.
= 332.8 Å		0.83 Å/pix.
x 400 pix.
= 332.8 Å

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Voxel sizeX=Y=Z: 0.832 Å
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Contour LevelBy AUTHOR: 0.0066
Minimum - Maximum-0.0073822634 - 0.03700003
Average (Standard dev.)0.000206077 (±0.0018447845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51217_msk_1.map
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Additional map: #1

Fileemd_51217_additional_1.map
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Half map: #1

Fileemd_51217_half_map_1.map
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Half map: #2

Fileemd_51217_half_map_2.map
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Sample components

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Entire : Structure of Edeine-30S-IF1-IF3-mRNA-tRNA translation pre-initiat...

EntireName: Structure of Edeine-30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex, open form
Components
  • Complex: Structure of Edeine-30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex, open form

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Supramolecule #1: Structure of Edeine-30S-IF1-IF3-mRNA-tRNA translation pre-initiat...

SupramoleculeName: Structure of Edeine-30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex, open form
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#7, #9-#16, #1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 850 KDa

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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: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.14 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.1 µm / Nominal defocus min: 0.3 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:

8cep

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82223
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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