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Yorodumi- EMDB-27535: Cryo-EM structure of the ribosome-bound Bacteroides thetaiotaomic... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27535 | |||||||||
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Title | Cryo-EM structure of the ribosome-bound Bacteroides thetaiotaomicron EF-G2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Translation elongation factor / Bacteroides thetaiotaomicron EF-G2 / TRANSLATION | |||||||||
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 | single particle reconstruction / Resolution: 4.0 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_27535.map.gz | 11.8 MB | EMDB map data format | |
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Header (meta data) | emd-27535-v30.xml emd-27535.xml | 15.5 KB 15.5 KB | Display Display | EMDB header |
Images | emd_27535.png | 59.6 KB | ||
Filedesc metadata | emd-27535.cif.gz | 5.7 KB | ||
Others | emd_27535_half_map_1.map.gz emd_27535_half_map_2.map.gz | 11.9 MB 11.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27535 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27535 | HTTPS FTP |
-Validation report
Summary document | emd_27535_validation.pdf.gz | 727.4 KB | Display | EMDB validaton report |
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Full document | emd_27535_full_validation.pdf.gz | 726.9 KB | Display | |
Data in XML | emd_27535_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | emd_27535_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27535 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27535 | HTTPS FTP |
-Related structure data
Related structure data | 8dmfMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27535.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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: #2
File | emd_27535_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27535_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 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria) |
-Macromolecule #1: Tetracycline resistance protein TetQ
Macromolecule | Name: Tetracycline resistance protein TetQ / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria) Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50 |
Molecular weight | Theoretical: 80.353859 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MKVYQTNEIK NIALLGSSGS GKTTLVEAML FESGVIKRRG SVAAKNTVSD YFPVEQEYGY SVFSTVLHVE WNNKKLNIID CPGSDDFVG STVTALNVTD TAIILLNGQY GVEVGTQNHF RYTEKLNKPV IFLVNQLDNE KCDYDNILEQ LKEAYGSKVV P IQYPIATG ...String: MKVYQTNEIK NIALLGSSGS GKTTLVEAML FESGVIKRRG SVAAKNTVSD YFPVEQEYGY SVFSTVLHVE WNNKKLNIID CPGSDDFVG STVTALNVTD TAIILLNGQY GVEVGTQNHF RYTEKLNKPV IFLVNQLDNE KCDYDNILEQ LKEAYGSKVV P IQYPIATG PGFNALIDVL LMKKYSWKPE GGAPVIEDIP AEEMDKAMEM HKALVEAAAE NDEGLMEKFF EQDSLTEDEM RE GIRKGLI ARGMFPVFCV CGGKDMGVRR LMEFLGNVVP FVSEMPKVEN TDGKEVAPDV NGPESLYFFK TSVEPHIGEV SYF KVMSGK VREGDDLLNA DRGSKERIAQ IYVVAGGNRV KVEELQAGDI GAAVKLKDVK TGNTLNGKDC DYKFNFIKYP NSKY SRAIK PVNEADVEKM MTILNRMREE DPTWVIEQSK ELKQTLVHGQ GEFHLRTLKW RLENNEKLQV KFEEPKIPYR ETITK AARA DYRHKKQSGG AGQFGEVHLI VEPYKEGMPV PDTYKFNGQE FKITVRGTEE IPLEWGGKLV FINSIVGGSI DARFLP AIM KGIMSRLEQG PLTGSYARDV RVIVYDGKMH PVDSNEISFM LAGRNAFSEA FKNAGPKILE PIYDVEVFVP SDRMGDV MG DLQGRRAMIM GMSSEKGFEK LVAKVPLKEM SSYSTALSSL TGGRASFIMK FASYELVPTD VQDKLIKDFE AKQTEE UniProtKB: Tetracycline resistance protein TetQ |
-Macromolecule #2: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-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
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134023 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |