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- EMDB-13808: 30S-head SSU focused-refinement of the erythromycin-stalled Esche... -

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Basic information

Entry
Database: EMDB / ID: EMD-13808
Title30S-head SSU focused-refinement of the erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain
Map data30S-head SSU focused-refinement of the erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain
Sample
  • Complex: Erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain
    • Complex: Erythromycin-stalled Escherichia coli 70S ribosome
    • Complex: streptococcal mRNA and MsrDL nascent chain
KeywordsRibosome / protein synthesis / antibiotic resistance / ARE ABC-F protein family / leader peptide / cryo-EM
Biological speciesEscherichia coli (E. coli) / Streptococcus pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsFostier CR / Ousalem F / Soufari H / Leroy EC / Saravuth N / Innis A / Hashem Y / Boel G
Funding support France, 2 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE35-0010 France
Agence Nationale de la Recherche (ANR)ANR-14-ACHN-0027 France
CitationJournal: Nat Commun / Year: 2023
Title: Regulation of the macrolide resistance ABC-F translation factor MsrD.
Authors: Corentin R Fostier / Farès Ousalem / Elodie C Leroy / Saravuth Ngo / Heddy Soufari / C Axel Innis / Yaser Hashem / Grégory Boël /
Abstract: Antibiotic resistance ABC-Fs (ARE ABC-Fs) are translation factors that provide resistance against clinically important ribosome-targeting antibiotics which are proliferating among pathogens. Here, we ...Antibiotic resistance ABC-Fs (ARE ABC-Fs) are translation factors that provide resistance against clinically important ribosome-targeting antibiotics which are proliferating among pathogens. Here, we combine genetic and structural approaches to determine the regulation of streptococcal ARE ABC-F gene msrD in response to macrolide exposure. We show that binding of cladinose-containing macrolides to the ribosome prompts insertion of the leader peptide MsrDL into a crevice of the ribosomal exit tunnel, which is conserved throughout bacteria and eukaryotes. This leads to a local rearrangement of the 23 S rRNA that prevents peptide bond formation and accommodation of release factors. The stalled ribosome obstructs the formation of a Rho-independent terminator structure that prevents msrD transcriptional attenuation. Erythromycin induction of msrD expression via MsrDL, is suppressed by ectopic expression of mrsD, but not by mutants which do not provide antibiotic resistance, showing correlation between MsrD function in antibiotic resistance and its action on this stalled complex.
History
DepositionOct 31, 2021-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13808.png

Downloads & links

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Map

FileDownload / File: emd_13808.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation30S-head SSU focused-refinement of the erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 360 pix.
= 414. Å		1.15 Å/pix.
x 360 pix.
= 414. Å		1.15 Å/pix.
x 360 pix.
= 414. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.038185477 - 0.095746
Average (Standard dev.)0.00007377734 (±0.0015197647)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 414.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Erythromycin-stalled Escherichia coli 70S ribosome with streptoco...

EntireName: Erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain
Components
  • Complex: Erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain
    • Complex: Erythromycin-stalled Escherichia coli 70S ribosome
    • Complex: streptococcal mRNA and MsrDL nascent chain

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Supramolecule #1: Erythromycin-stalled Escherichia coli 70S ribosome with streptoco...

SupramoleculeName: Erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#56

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Supramolecule #2: Erythromycin-stalled Escherichia coli 70S ribosome

SupramoleculeName: Erythromycin-stalled Escherichia coli 70S ribosome / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: streptococcal mRNA and MsrDL nascent chain

SupramoleculeName: streptococcal mRNA and MsrDL nascent chain / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Streptococcus pneumoniae (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

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6tbv

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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