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- EMDB-71908: QS 70S ribosome purified from FN200 cells -

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Basic information

Entry
Database: EMDB / ID: EMD-71908
TitleQS 70S ribosome purified from FN200 cells
Map data
Sample
  • Complex: QS 70S ribosome purified from FN200 cells
KeywordsRibosome / 70S / Initiation complex / translation / QS
Biological speciesFlavobacterium johnsoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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: Role of the anti-Shine-Dalgarno sequence of 16S rRNA in Flavobacterium johnsoniae.
Authors: Fawwaz M Naeem / Bappaditya Roy / Dominic Arpin / Zakkary A McNutt / Kyung-Mee Moon / Bryan T Gemler / Ralf Bundschuh / Leonard J Foster / Joaquin Ortega / Kurt Fredrick /
Abstract: Bacteroidia ribosomes are "blind" to Shine-Dalgarno (SD) sequences because the anti-SD (ASD) of 16S rRNA is sequestered by bS21, bS18, and bS6 on the 30S platform. In Flavobacterium johnsoniae, one ...Bacteroidia ribosomes are "blind" to Shine-Dalgarno (SD) sequences because the anti-SD (ASD) of 16S rRNA is sequestered by bS21, bS18, and bS6 on the 30S platform. In Flavobacterium johnsoniae, one gene contains a strong SD sequence-rpsU, which encodes bS21. Flavobacterium johnsoniae ribosomes lacking bS21 translate rpsU at a higher rate, which establishes an autoregulatory cycle. Here, we targeted the ASD of 16S rRNA in F. johnsoniae, ablating the core element (CCUCC to GAAGC). Replacement of each 16S gene with this quadruple-substituted (QS) allele had little effect until the last gene was changed. The final strain, containing only QS ribosomes, grows poorly. This defect can be largely rescued by replacing the translation initiation region (TIR) of rpsU with the SD-less TIR of tuf. Purified QS ribosomes fail to translate native rpsU messenger RNA (mRNA) but are active on SD-less mRNAs. We also selected suppressors of the ASD-ablated strain, many of which carried a point mutation in the SD of rpsU. Such mutations increase bS21 synthesis in the ASD-ablated strain but reduce bS21 synthesis by wild-type ribosomes, underscoring the importance of SD-ASD pairing in the natural case. We also find that ASD ablation inhibits rRNA processing, an effect independent of bS21.
History
DepositionAug 4, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71908.png

Downloads & links

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Map

FileDownload / File: emd_71908.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 (log scale)
Contour LevelBy AUTHOR: 0.0787
Minimum - Maximum-0.084478386 - 0.35538283
Average (Standard dev.)0.0028444896 (±0.016890049)
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: #2

Fileemd_71908_additional_1.map
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Additional map: #1

Fileemd_71908_additional_2.map
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Half map: #2

Fileemd_71908_half_map_1.map
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Half map: #1

Fileemd_71908_half_map_2.map
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Sample components

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Entire : QS 70S ribosome purified from FN200 cells

EntireName: QS 70S ribosome purified from FN200 cells
Components
  • Complex: QS 70S ribosome purified from FN200 cells

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Supramolecule #1: QS 70S ribosome purified from FN200 cells

SupramoleculeName: QS 70S ribosome purified from FN200 cells / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#54, #1-#2
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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 241290
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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