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Yorodumi- EMDB-0939: The Structural Basis for Inhibition of Ribosome Translocation by ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0939 | |||||||||
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Title | The Structural Basis for Inhibition of Ribosome Translocation by Viomycin | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 3.7 Å | |||||||||
Authors | Zhang L / Wang YH / Zhang X / Lancaster L / Zhou J / Noller HF | |||||||||
Funding support | China, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: The structural basis for inhibition of ribosomal translocation by viomycin. Authors: Ling Zhang / Ying-Hui Wang / Xing Zhang / Laura Lancaster / Jie Zhou / Harry F Noller / Abstract: Viomycin, an antibiotic that has been used to fight tuberculosis infections, is believed to block the translocation step of protein synthesis by inhibiting ribosomal subunit dissociation and trapping ...Viomycin, an antibiotic that has been used to fight tuberculosis infections, is believed to block the translocation step of protein synthesis by inhibiting ribosomal subunit dissociation and trapping the ribosome in an intermediate state of intersubunit rotation. The mechanism by which viomycin stabilizes this state remains unexplained. To address this, we have determined cryo-EM and X-ray crystal structures of 70S ribosome complexes trapped in a rotated state by viomycin. The 3.8-Å resolution cryo-EM structure reveals a ribosome trapped in the hybrid state with 8.6° intersubunit rotation and 5.3° rotation of the 30S subunit head domain, bearing a single P/E state transfer RNA (tRNA). We identify five different binding sites for viomycin, four of which have not been previously described. To resolve the details of their binding interactions, we solved the 3.1-Å crystal structure of a viomycin-bound ribosome complex, revealing that all five viomycins bind to ribosomal RNA. One of these (Vio1) corresponds to the single viomycin that was previously identified in a complex with a nonrotated classical-state ribosome. Three of the newly observed binding sites (Vio3, Vio4, and Vio5) are clustered at intersubunit bridges, consistent with the ability of viomycin to inhibit subunit dissociation. We propose that one or more of these same three viomycins induce intersubunit rotation by selectively binding the rotated state of the ribosome at dynamic elements of 16S and 23S rRNA, thus, blocking conformational changes associated with molecular movements that are required for translocation. | |||||||||
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_0939.map.gz | 116.1 MB | EMDB map data format | |
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Header (meta data) | emd-0939-v30.xml emd-0939.xml | 7.9 KB 7.9 KB | Display Display | EMDB header |
Images | emd_0939.png | 77.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0939 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0939 | HTTPS FTP |
-Validation report
Summary document | emd_0939_validation.pdf.gz | 78.7 KB | Display | EMDB validaton report |
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Full document | emd_0939_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_0939_validation.xml.gz | 491 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0939 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0939 | HTTPS FTP |
-Related 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_0939.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.014 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 : Structure of ribosome-viomycin complex
Entire | Name: Structure of ribosome-viomycin complex |
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Components |
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-Supramolecule #1: Structure of ribosome-viomycin complex
Supramolecule | Name: Structure of ribosome-viomycin complex / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7 |
Staining | Type: NONE / Material: no |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 130000 |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |