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Yorodumi- EMDB-8176: Cryo-EM structure of an ErmBL-stalled ribosome in complex with P-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8176 | |||||||||
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Title | Cryo-EM structure of an ErmBL-stalled ribosome in complex with P-, and E-tRNA | |||||||||
Map data | None | |||||||||
Sample |
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Function / homology | Function and homology information stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis ...stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / DNA endonuclease activity / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / large ribosomal subunit / ribosome biogenesis / small ribosomal subunit rRNA binding / ribosome binding / ribosomal large subunit assembly / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / 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) / Escherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Arenz S / Bock LV / Graf M / Innis CA / Beckmann R / Grubmueller H / Vaiana AC / Wilson DN | |||||||||
Citation | Journal: Nat Commun / Year: 2016 Title: A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest. Authors: Stefan Arenz / Lars V Bock / Michael Graf / C Axel Innis / Roland Beckmann / Helmut Grubmüller / Andrea C Vaiana / Daniel N Wilson / Abstract: Nascent polypeptides can induce ribosome stalling, regulating downstream genes. Stalling of ErmBL peptide translation in the presence of the macrolide antibiotic erythromycin leads to resistance in ...Nascent polypeptides can induce ribosome stalling, regulating downstream genes. Stalling of ErmBL peptide translation in the presence of the macrolide antibiotic erythromycin leads to resistance in Streptococcus sanguis. To reveal this stalling mechanism we obtained 3.6-Å-resolution cryo-EM structures of ErmBL-stalled ribosomes with erythromycin. The nascent peptide adopts an unusual conformation with the C-terminal Asp10 side chain in a previously unseen rotated position. Together with molecular dynamics simulations, the structures indicate that peptide-bond formation is inhibited by displacement of the peptidyl-tRNA A76 ribose from its canonical position, and by non-productive interactions of the A-tRNA Lys11 side chain with the A-site crevice. These two effects combine to perturb peptide-bond formation by increasing the distance between the attacking Lys11 amine and the Asp10 carbonyl carbon. The interplay between drug, peptide and ribosome uncovered here also provides insight into the fundamental mechanism of peptide-bond formation. | |||||||||
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_8176.map.gz | 176.3 MB | EMDB map data format | |
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Header (meta data) | emd-8176-v30.xml emd-8176.xml | 65.5 KB 65.5 KB | Display Display | EMDB header |
Images | emd_8176.png | 38.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8176 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8176 | HTTPS FTP |
-Validation report
Summary document | emd_8176_validation.pdf.gz | 303.4 KB | Display | EMDB validaton report |
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Full document | emd_8176_full_validation.pdf.gz | 302.5 KB | Display | |
Data in XML | emd_8176_validation.xml.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8176 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8176 | HTTPS FTP |
-Related structure data
Related structure data | 5ju8MC 8175C 5jteC 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_8176.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
+Entire : ErmBL-stalled E.coli 70S ribosome
+Supramolecule #1: ErmBL-stalled E.coli 70S ribosome
+Macromolecule #1: 16S ribosomal RNA
+Macromolecule #22: mRNA
+Macromolecule #23: P-site tRNA Aspartate
+Macromolecule #24: E-site tRNA Valine
+Macromolecule #25: 23S ribosomal RNA
+Macromolecule #26: 5S ribosomal RNA
+Macromolecule #2: 30S ribosomal protein S2
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: 30S ribosomal protein S4
+Macromolecule #5: 30S ribosomal protein S5
+Macromolecule #6: 30S ribosomal protein S6
+Macromolecule #7: 30S ribosomal protein S7
+Macromolecule #8: 30S ribosomal protein S8
+Macromolecule #9: 30S ribosomal protein S9
+Macromolecule #10: 30S ribosomal protein S10
+Macromolecule #11: 30S ribosomal protein S11
+Macromolecule #12: 30S ribosomal protein S12
+Macromolecule #13: 30S ribosomal protein S13
+Macromolecule #14: 30S ribosomal protein S14
+Macromolecule #15: 30S ribosomal protein S15
+Macromolecule #16: 30S ribosomal protein S16
+Macromolecule #17: 30S ribosomal protein S17
+Macromolecule #18: 30S ribosomal protein S18
+Macromolecule #19: 30S ribosomal protein S19
+Macromolecule #20: 30S ribosomal protein S20
+Macromolecule #21: 30S ribosomal protein S21
+Macromolecule #27: 50S ribosomal protein L2
+Macromolecule #28: 50S ribosomal protein L3
+Macromolecule #29: 50S ribosomal protein L4
+Macromolecule #30: 50S ribosomal protein L5
+Macromolecule #31: 50S ribosomal protein L6
+Macromolecule #32: 50S ribosomal protein L9
+Macromolecule #33: 50S ribosomal protein L11
+Macromolecule #34: 50S ribosomal protein L13
+Macromolecule #35: 50S ribosomal protein L14
+Macromolecule #36: 50S ribosomal protein L15
+Macromolecule #37: 50S ribosomal protein L16
+Macromolecule #38: 50S ribosomal protein L17
+Macromolecule #39: 50S ribosomal protein L18
+Macromolecule #40: 50S ribosomal protein L19
+Macromolecule #41: 50S ribosomal protein L20
+Macromolecule #42: 50S ribosomal protein L21
+Macromolecule #43: 50S ribosomal protein L22
+Macromolecule #44: 50S ribosomal protein L23
+Macromolecule #45: 50S ribosomal protein L24
+Macromolecule #46: 50S ribosomal protein L25
+Macromolecule #47: 50S ribosomal protein L27
+Macromolecule #48: 50S ribosomal protein L28
+Macromolecule #49: 50S ribosomal protein L29
+Macromolecule #50: 50S ribosomal protein L30
+Macromolecule #51: 50S ribosomal protein L32
+Macromolecule #52: 50S ribosomal protein L33
+Macromolecule #53: 50S ribosomal protein L34
+Macromolecule #54: 50S ribosomal protein L35
+Macromolecule #55: 50S ribosomal protein L36
+Macromolecule #56: ErmBL
+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: 7.4 |
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Sugar embedding | Material: vitreous ice |
Grid | Model: Quantifoil R3/3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 4.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.7 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 4) |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF Details: Due to image processing in the absence of spatial frequencies higher than 8 angstroms, the FSC value of 0.143 was used for average resolution determination. Number images used: 85393 |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: SPIDER |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: SPIDER |