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- EMDB-71567: Flavobacterium johnsoniae bS6 C-terminal deletion mutant 70S ribosome. -

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Basic information

Entry
Database: EMDB / ID: EMD-71567
TitleFlavobacterium johnsoniae bS6 C-terminal deletion mutant 70S ribosome.
Map data
Sample
  • Complex: Flavobacterium johnsoniae bS6 C-terminal deletion mutant 70S ribosome.
KeywordsRibosome / initiation complex / Flavobacterium johnsoniae
Biological speciesFlavobacterium johnsoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsOrtega J / Arpin D
Funding support Canada, 1 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structure of a specialized 70S initiation complex.
Authors: Dominic Arpin / Bappaditya Roy / Fawwaz M Naeem / Kurt Fredrick / Joaquin Ortega /
Abstract: Bacteria of class Bacteroidia lack Shine-Dalgarno (SD) sequences and instead rely on other messenger RNA (mRNA) features, including upstream adenines, for start codon selection. Bacteroidia ribosomes ...Bacteria of class Bacteroidia lack Shine-Dalgarno (SD) sequences and instead rely on other messenger RNA (mRNA) features, including upstream adenines, for start codon selection. Bacteroidia ribosomes contain the anti-SD (ASD) sequence of 16S ribosomal RNA (rRNA) but are "blind" to SD sequences. This occurs due to the sequestration of the ASD through interactions with bS21, bS18, and bS6 on the 30S platform domain. In many Bacteroidia, including Flavobacterium johnsoniae, there is one gene with an extended SD-rpsU, which encodes bS21. Ribosomes lacking bS21 exhibit high-level translation of rpsU, establishing an autoregulatory circuit in the cell. In this work, we investigate the structural basis of initiation on rpsU mRNA. We find using cryo-electron microscopy that initiation entails the formation of a 13-base pair SD-ASD helix that sterically occludes bS21. Mutations of bS21, bS18, or bS6 that compromise the platform pocket liberate the 3' tail of 16S rRNA, enable SD-ASD pairing, and enhance initiation. As initiation on rpsU mRNA depends on SD-ASD pairing, we infer that dissociation of bS21 from replete ribosomes limits their initiation rate. This work shows how a compositional change of the ribosome can govern translation of a specific gene.
History
DepositionJul 2, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71567.png

Downloads & links

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Map

FileDownload / File: emd_71567.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 480 pix.
= 410.4 Å		0.86 Å/pix.
x 480 pix.
= 410.4 Å		0.86 Å/pix.
x 480 pix.
= 410.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0806
Minimum - Maximum-0.094206065 - 0.4235391
Average (Standard dev.)0.0031958828 (±0.018769013)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 410.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_71567_additional_1.map
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Half map: #1

Fileemd_71567_half_map_1.map
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Half map: #2

Fileemd_71567_half_map_2.map
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Sample components

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Entire : Flavobacterium johnsoniae bS6 C-terminal deletion mutant 70S ribosome.

EntireName: Flavobacterium johnsoniae bS6 C-terminal deletion mutant 70S ribosome.
Components
  • Complex: Flavobacterium johnsoniae bS6 C-terminal deletion mutant 70S ribosome.

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Supramolecule #1: Flavobacterium johnsoniae bS6 C-terminal deletion mutant 70S ribosome.

SupramoleculeName: Flavobacterium johnsoniae bS6 C-terminal deletion mutant 70S ribosome.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12, #14-#56
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 346476
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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