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- EMDB-27535: Cryo-EM structure of the ribosome-bound Bacteroides thetaiotaomic... -

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Basic information

Entry
Database: EMDB / ID: EMD-27535
TitleCryo-EM structure of the ribosome-bound Bacteroides thetaiotaomicron EF-G2
Map data
Sample
  • Complex: ribosome-bound Bacteroides thetaiotaomicron EF-G2
    • Protein or peptide: Tetracycline resistance protein TetQ
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
KeywordsTranslation 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
: / Elongation factor G domain 2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV ...: / Elongation factor G domain 2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
Methodsingle particle reconstruction / Resolution: 4.0 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-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27535.png

Downloads & links

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Map

FileDownload / File: emd_27535.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 160 pix.
= 170.88 Å		1.07 Å/pix.
x 160 pix.
= 170.88 Å		1.07 Å/pix.
x 160 pix.
= 170.88 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.030693619 - 0.04475163
Average (Standard dev.)-0.0013912932 (±0.0031523951)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 170.87999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27535_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27535_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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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
    • Protein or peptide: Tetracycline resistance protein TetQ
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE

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

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

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Macromolecule #1: Tetracycline resistance protein TetQ

MacromoleculeName: Tetracycline resistance protein TetQ / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50
Molecular weightTheoretical: 80.353859 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: 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: Elongation factor G

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134023
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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