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Yorodumi- EMDB-12574: Structure of ErmDL-Erythromycin-stalled 70S E. coli ribosomal com... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12574 | |||||||||
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Title | Structure of ErmDL-Erythromycin-stalled 70S E. coli ribosomal complex with A and P-tRNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Antibiotic / ErmDL / Erythromycin / Macrolide / Stalling / RIBOSOME | |||||||||
Function / homology | Function and homology information transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly ...transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Beckert B / Wilson DN | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics. Authors: Bertrand Beckert / Elodie C Leroy / Shanmugapriya Sothiselvam / Lars V Bock / Maxim S Svetlov / Michael Graf / Stefan Arenz / Maha Abdelshahid / Britta Seip / Helmut Grubmüller / Alexander ...Authors: Bertrand Beckert / Elodie C Leroy / Shanmugapriya Sothiselvam / Lars V Bock / Maxim S Svetlov / Michael Graf / Stefan Arenz / Maha Abdelshahid / Britta Seip / Helmut Grubmüller / Alexander S Mankin / C Axel Innis / Nora Vázquez-Laslop / Daniel N Wilson / Abstract: Macrolides and ketolides comprise a family of clinically important antibiotics that inhibit protein synthesis by binding within the exit tunnel of the bacterial ribosome. While these antibiotics are ...Macrolides and ketolides comprise a family of clinically important antibiotics that inhibit protein synthesis by binding within the exit tunnel of the bacterial ribosome. While these antibiotics are known to interrupt translation at specific sequence motifs, with ketolides predominantly stalling at Arg/Lys-X-Arg/Lys motifs and macrolides displaying a broader specificity, a structural basis for their context-specific action has been lacking. Here, we present structures of ribosomes arrested during the synthesis of an Arg-Leu-Arg sequence by the macrolide erythromycin (ERY) and the ketolide telithromycin (TEL). Together with deep mutagenesis and molecular dynamics simulations, the structures reveal how ERY and TEL interplay with the Arg-Leu-Arg motif to induce translational arrest and illuminate the basis for the less stringent sequence-specific action of ERY over TEL. Because programmed stalling at the Arg/Lys-X-Arg/Lys motifs is used to activate expression of antibiotic resistance genes, our study also provides important insights for future development of improved macrolide antibiotics. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12574.map.gz | 21.9 MB | EMDB map data format | |
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Header (meta data) | emd-12574-v30.xml emd-12574.xml | 76.3 KB 76.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12574_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_12574.png | 194.1 KB | ||
Filedesc metadata | emd-12574.cif.gz | 13.5 KB | ||
Others | emd_12574_additional_1.map.gz emd_12574_additional_2.map.gz emd_12574_half_map_1.map.gz emd_12574_half_map_2.map.gz | 86.5 MB 138.6 MB 140.7 MB 140.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12574 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12574 | HTTPS FTP |
-Validation report
Summary document | emd_12574_validation.pdf.gz | 922.3 KB | Display | EMDB validaton report |
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Full document | emd_12574_full_validation.pdf.gz | 921.8 KB | Display | |
Data in XML | emd_12574_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | emd_12574_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12574 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12574 | HTTPS FTP |
-Related structure data
Related structure data | 7nspMC 7nsoC 7nsqC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12574.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.108 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Map Filtered according to local Resolution
File | emd_12574_additional_1.map | ||||||||||||
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Annotation | Map Filtered according to local Resolution | ||||||||||||
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Density Histograms |
-Additional map: relion final run DC1
File | emd_12574_additional_2.map | ||||||||||||
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Annotation | relion final run DC1 | ||||||||||||
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Density Histograms |
-Half map: Half map 1
File | emd_12574_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_12574_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Structure of ErmDL-Erythromycin-stalled 70S E. coli ribosomal com...
+Supramolecule #1: Structure of ErmDL-Erythromycin-stalled 70S E. coli ribosomal com...
+Macromolecule #1: 23S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #32: mRNA
+Macromolecule #34: P-tRNA (leu)
+Macromolecule #35: 16S rRNA
+Macromolecule #56: A-tRNA (Arg)
+Macromolecule #3: 50S ribosomal protein L2
+Macromolecule #4: 50S ribosomal protein L3
+Macromolecule #5: 50S ribosomal protein L4
+Macromolecule #6: 50S ribosomal protein L5
+Macromolecule #7: 50S ribosomal protein L6
+Macromolecule #8: 50S ribosomal protein L9
+Macromolecule #9: 50S ribosomal protein L13
+Macromolecule #10: 50S ribosomal protein L14
+Macromolecule #11: 50S ribosomal protein L15
+Macromolecule #12: 50S ribosomal protein L16
+Macromolecule #13: 50S ribosomal protein L17
+Macromolecule #14: 50S ribosomal protein L18
+Macromolecule #15: 50S ribosomal protein L19
+Macromolecule #16: 50S ribosomal protein L20
+Macromolecule #17: 50S ribosomal protein L21
+Macromolecule #18: 50S ribosomal protein L22
+Macromolecule #19: 50S ribosomal protein L23
+Macromolecule #20: 50S ribosomal protein L24
+Macromolecule #21: 50S ribosomal protein L25
+Macromolecule #22: 50S ribosomal protein L27
+Macromolecule #23: 50S ribosomal protein L28
+Macromolecule #24: 50S ribosomal protein L29
+Macromolecule #25: 50S ribosomal protein L30
+Macromolecule #26: 50S ribosomal protein L32
+Macromolecule #27: 50S ribosomal protein L33
+Macromolecule #28: 50S ribosomal protein L34
+Macromolecule #29: 50S ribosomal protein L35
+Macromolecule #30: 50S ribosomal protein L36
+Macromolecule #31: 50S ribosomal protein L31
+Macromolecule #33: ermDL
+Macromolecule #36: 30S ribosomal protein S2
+Macromolecule #37: 30S ribosomal protein S3
+Macromolecule #38: 30S ribosomal protein S4
+Macromolecule #39: 30S ribosomal protein S5
+Macromolecule #40: 30S ribosomal protein S6
+Macromolecule #41: 30S ribosomal protein S7
+Macromolecule #42: 30S ribosomal protein S8
+Macromolecule #43: 30S ribosomal protein S9
+Macromolecule #44: 30S ribosomal protein S10
+Macromolecule #45: 30S ribosomal protein S11
+Macromolecule #46: 30S ribosomal protein S12
+Macromolecule #47: 30S ribosomal protein S13
+Macromolecule #48: 30S ribosomal protein S14
+Macromolecule #49: 30S ribosomal protein S15
+Macromolecule #50: 30S ribosomal protein S16
+Macromolecule #51: 30S ribosomal protein S17
+Macromolecule #52: 30S ribosomal protein S18
+Macromolecule #53: 30S ribosomal protein S19
+Macromolecule #54: 30S ribosomal protein S20
+Macromolecule #55: 30S ribosomal protein S21
+Macromolecule #57: ERYTHROMYCIN A
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R3/3 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 300 |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Average exposure time: 35.0 sec. / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-7nsp: |