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Yorodumi- EMDB-13806: 50S LSU focused-refinement of the erythromycin-stalled Escherichi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13806 | |||||||||
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Title | 50S LSU focused-refinement of the erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain | |||||||||
Map data | 50S LSU focused-refinement of the erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain | |||||||||
Sample |
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Keywords | Ribosome / protein synthesis / antibiotic resistance / ARE ABC-F protein family / leader peptide / cryo-EM | |||||||||
Biological species | Escherichia coli (E. coli) / Streptococcus pneumoniae (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.97 Å | |||||||||
Authors | Fostier CR / Ousalem F / Soufari H / Leroy EC / Saravuth N / Innis A / Hashem Y / Boel G | |||||||||
Funding support | France, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13806.map.gz | 7.9 MB | EMDB map data format | |
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Header (meta data) | emd-13806-v30.xml emd-13806.xml | 16.8 KB 16.8 KB | Display Display | EMDB header |
Images | emd_13806.png | 82.9 KB | ||
Filedesc metadata | emd-13806.cif.gz | 3.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13806 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13806 | HTTPS FTP |
-Validation report
Summary document | emd_13806_validation.pdf.gz | 423.3 KB | Display | EMDB validaton report |
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Full document | emd_13806_full_validation.pdf.gz | 422.8 KB | Display | |
Data in XML | emd_13806_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | emd_13806_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13806 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13806 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13806.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | 50S LSU focused-refinement of the erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Erythromycin-stalled Escherichia coli 70S ribosome with streptoco...
Entire | Name: Erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain |
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Components |
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-Supramolecule #1: Erythromycin-stalled Escherichia coli 70S ribosome with streptoco...
Supramolecule | Name: 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
Supramolecule | Name: Erythromycin-stalled Escherichia coli 70S ribosome / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Supramolecule #3: streptococcal mRNA and MsrDL nascent chain
Supramolecule | Name: streptococcal mRNA and MsrDL nascent chain / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Streptococcus pneumoniae (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75000 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |