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- EMDB-27547: Cryo-EM structure of E. coli ribosome associated with Bacteroides... -

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Basic information

Entry
Database: EMDB / ID: EMD-27547
TitleCryo-EM structure of E. coli ribosome associated with Bacteroides thetaiotaomicron EF-G2 from focused 3D refinement
Map data
Sample
  • Complex: ribosome-bound Bacteroides thetaiotaomicron EF-G2
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
Methodsingle particle reconstruction / Resolution: 3.0 Å
AuthorsWang C / Han W / Groisman EA / Liu J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: 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
DepositionJul 8, 2022-
Header (metadata) releaseJan 4, 2023-
Map releaseJan 4, 2023-
UpdateJan 4, 2023-
Current statusJan 4, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27547.png

Downloads & links

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Map

FileDownload / File: emd_27547.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 341.76 Å		1.07 Å/pix.
x 320 pix.
= 341.76 Å		1.07 Å/pix.
x 320 pix.
= 341.76 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.022736311 - 0.068573445
Average (Standard dev.)0.00015681374 (±0.0017340281)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 341.75998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_27547_half_map_1.map
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Half map: #2

Fileemd_27547_half_map_2.map
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Sample components

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Entire : ribosome-bound Bacteroides thetaiotaomicron EF-G2

EntireName: ribosome-bound Bacteroides thetaiotaomicron EF-G2
Components
  • Complex: ribosome-bound Bacteroides thetaiotaomicron EF-G2

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Supramolecule #1: ribosome-bound Bacteroides thetaiotaomicron EF-G2

SupramoleculeName: ribosome-bound Bacteroides thetaiotaomicron EF-G2 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63782
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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