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Yorodumi- PDB-8dmf: Cryo-EM structure of the ribosome-bound Bacteroides thetaiotaomic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dmf | ||||||
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Title | Cryo-EM structure of the ribosome-bound Bacteroides thetaiotaomicron EF-G2 | ||||||
Components | Tetracycline resistance protein TetQ | ||||||
Keywords | TRANSLATION / Translation elongation factor / Bacteroides thetaiotaomicron EF-G2 | ||||||
Function / homology | Function and homology information ribosome disassembly / translation elongation factor activity / GTPase activity / GTP binding Similarity search - Function | ||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / Resolution: 4 Å | ||||||
Authors | Wang, C. / Han, W. / Groisman, E.A. / Liu, J. | ||||||
Funding support | United States, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dmf.cif.gz | 136.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dmf.ent.gz | 105.5 KB | Display | PDB format |
PDBx/mmJSON format | 8dmf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dmf_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8dmf_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8dmf_validation.xml.gz | 30 KB | Display | |
Data in CIF | 8dmf_validation.cif.gz | 42.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/8dmf ftp://data.pdbj.org/pub/pdb/validation_reports/dm/8dmf | HTTPS FTP |
-Related structure data
Related structure data | 27535MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 80353.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50 Gene: BT_2167 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8A5S1 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GTP / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ribosome-bound Bacteroides thetaiotaomicron EF-G2 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria) |
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 134023 / Symmetry type: POINT | ||||||||||||||||||||||||
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