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Yorodumi- EMDB-27546: Another class of E. coli ribosome associated with Bacteroides the... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27546 | |||||||||
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Title | Another class of E. coli ribosome associated with Bacteroides thetaiotaomicron EF-G2 | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | |||||||||
Method | single particle reconstruction / Resolution: 3.0 Å | |||||||||
Authors | Wang C / Han W / Groisman EA / Liu J | |||||||||
Funding support | United States, 1 items
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Citation | Journal: EMBO J / Year: 2023 Title: Gut colonization by Bacteroides requires translation by an EF-G paralog lacking GTPase activity. Authors: Weiwei Han / Bee-Zen Peng / Chunyan Wang / Guy E Townsend / Natasha A Barry / Frank Peske / Andrew L Goodman / Jun Liu / Marina V Rodnina / Eduardo A Groisman / Abstract: Protein synthesis is crucial for cell growth and survival yet one of the most energy-consuming cellular processes. How, then, do cells sustain protein synthesis under starvation conditions when ...Protein synthesis is crucial for cell growth and survival yet one of the most energy-consuming cellular processes. How, then, do cells sustain protein synthesis under starvation conditions when energy is limited? To accelerate the translocation of mRNA-tRNAs through the ribosome, bacterial elongation factor G (EF-G) hydrolyzes energy-rich guanosine triphosphate (GTP) for every amino acid incorporated into a protein. Here, we identify an EF-G paralog-EF-G2-that supports translocation without hydrolyzing GTP in the gut commensal bacterium Bacteroides thetaiotaomicron. EF-G2's singular ability to sustain protein synthesis, albeit at slow rates, is crucial for bacterial gut colonization. EF-G2 is ~10-fold more abundant than canonical EF-G1 in bacteria harvested from murine ceca and, unlike EF-G1, specifically accumulates during carbon starvation. Moreover, we uncover a 26-residue region unique to EF-G2 that is essential for protein synthesis, EF-G2 dissociation from the ribosome, and responsible for the absence of GTPase activity. Our findings reveal how cells curb energy consumption while maintaining protein synthesis to advance fitness in nutrient-fluctuating environments. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27546.map.gz | 98.8 MB | EMDB map data format | |
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Header (meta data) | emd-27546-v30.xml emd-27546.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
Images | emd_27546.png | 72.7 KB | ||
Others | emd_27546_half_map_1.map.gz emd_27546_half_map_2.map.gz | 98.9 MB 98.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27546 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27546 | HTTPS FTP |
-Validation report
Summary document | emd_27546_validation.pdf.gz | 873.9 KB | Display | EMDB validaton report |
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Full document | emd_27546_full_validation.pdf.gz | 873.5 KB | Display | |
Data in XML | emd_27546_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | emd_27546_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27546 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27546 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27546.map.gz / Format: CCP4 / Size: 125 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: 1.068 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_27546_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27546_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ribosome-bound Bacteroides thetaiotaomicron EF-G2
Entire | Name: ribosome-bound Bacteroides thetaiotaomicron EF-G2 |
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Components |
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-Supramolecule #1: ribosome-bound Bacteroides thetaiotaomicron EF-G2
Supramolecule | Name: ribosome-bound Bacteroides thetaiotaomicron EF-G2 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria) |
-Experimental details
-Structure determination
Processing | single particle reconstruction |
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Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93541 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |