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Structure paper

TitleMechanistic insights into the alternative ribosome recycling by HflXr.
Journal, issue, pagesNucleic Acids Res, Vol. 52, Issue 7, Page 4053-4066, Year 2024
Publish dateApr 24, 2024
AuthorsSavannah M Seely / Ritwika S Basu / Matthieu G Gagnon /
PubMed AbstractDuring stress conditions such as heat shock and antibiotic exposure, ribosomes stall on messenger RNAs, leading to inhibition of protein synthesis. To remobilize ribosomes, bacteria use rescue ...During stress conditions such as heat shock and antibiotic exposure, ribosomes stall on messenger RNAs, leading to inhibition of protein synthesis. To remobilize ribosomes, bacteria use rescue factors such as HflXr, a homolog of the conserved housekeeping GTPase HflX that catalyzes the dissociation of translationally inactive ribosomes into individual subunits. Here we use time-resolved cryo-electron microscopy to elucidate the mechanism of ribosome recycling by Listeria monocytogenes HflXr. Within the 70S ribosome, HflXr displaces helix H69 of the 50S subunit and induces long-range movements of the platform domain of the 30S subunit, disrupting inter-subunit bridges B2b, B2c, B4, B7a and B7b. Our findings unveil a unique ribosome recycling strategy by HflXr which is distinct from that mediated by RRF and EF-G. The resemblance between HflXr and housekeeping HflX suggests that the alternative ribosome recycling mechanism reported here is universal in the prokaryotic kingdom.
External linksNucleic Acids Res / PubMed:38407413 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 3.8 Å
Structure data

42554

8uu4

EMDB-42554, PDB-8uu4:
Cryo-EM structure of the Listeria innocua 70S ribosome in complex with HPF (structure I-A)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-42555: Refined map of the Listeria innocua 70S ribosome (head-swiveled) in complex with pe/E-tRNA (structure I-B)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-42556: Focus refined map of the swiveled head domain of the 30S subunit of Listeria innocua ribosome (structure I-B)
Method: EM (single particle) / Resolution: 3.0 Å

42557

8uu5

EMDB-42557, PDB-8uu5:
Cryo-EM structure of the Listeria innocua 70S ribosome (head-swiveled) in complex with pe/E-tRNA (structure I-B)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-42558: Refined map of the ratcheted Listeria innocua 70S ribosome in complex with p/E-tRNA (structure II-A)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-42559: Focus refined map of the head domain of the ratcheted 30S subunit of Listeria innocua ribosome (structure II-A)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-42560: Focus refined map of the body domain of the ratcheted 30S subunit of Listeria innocua ribosome (structure II-A)
Method: EM (single particle) / Resolution: 3.2 Å

42561

8uu6

EMDB-42561, PDB-8uu6:
Cryo-EM structure of the ratcheted Listeria innocua 70S ribosome in complex with p/E-tRNA (structure II-A)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-42562: Refined map of the Listeria innocua 70S ribosome in complex with HflXr, HPF, and E-site tRNA (structure II-B)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-42563: Focus refined map of the head domain of the 30S subunit of Listeria innocua ribosome in complex with HflXr, HPF, and E-site tRNA (structure II-B)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-42564: Focus refined map of the body domain of the 30S subunit of Listeria innocua ribosome in complex with HflXr, HPF, and E-site tRNA (structure II-B)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-42565: Focus refined map of HflXr bound to the Listeria innocua ribosome in complex with HPF and E-site tRNA (structure II-B)
Method: EM (single particle) / Resolution: 3.8 Å

42566

8uu7

EMDB-42566, PDB-8uu7:
Cryo-EM structure of the Listeria innocua 70S ribosome in complex with HflXr, HPF, and E-site tRNA (structure II-B)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-42567: Refined map of the Listeria innocua 70S ribosome (head-swiveled) in complex with HflXr and pe/E-tRNA (structure II-C)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-42568: Focus refined map of the swiveled head domain of the 30S subunit of Listeria innocua ribosome in complex with HflXr and pe/E-tRNA (structure II-C)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-42569: Focus refined map of the body domain of the 30S subunit of Listeria innocua ribosome in complex with HflXr and pe/E-tRNA (structure II-C)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-42570: Focus refined map of HflXr bound to the Listeria innocua ribosome in complex with pe/E-tRNA (structure II-C)
Method: EM (single particle) / Resolution: 3.0 Å

42571

8uu8

EMDB-42571, PDB-8uu8:
Cryo-EM structure of the Listeria innocua 70S ribosome (head-swiveled) in complex with HflXr and pe/E-tRNA (structure II-C)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-42572: Refined map of the ratcheted Listeria innocua 70S ribosome (head-swiveled) in complex with HflXr and pe/E-tRNA (structure II-D)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-42573: Focus refined map of the swiveled head domain of the 30S subunit of ratcheted Listeria innocua ribosome in complex with HflXr and pe/E-tRNA (structure II-D)
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-42574: Focus refined map of the body domain of the 30S subunit of ratcheted Listeria innocua ribosome in complex with HflXr and pe/E-tRNA (structure II-D)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-42575: Focus refined map of HflXr bound to the ratcheted Listeria innocua ribosome in complex with pe/E-tRNA (structure II-D)
Method: EM (single particle) / Resolution: 3.0 Å

42576

8uu9

EMDB-42576, PDB-8uu9:
Cryo-EM structure of the ratcheted Listeria innocua 70S ribosome (head-swiveled) in complex with HflXr and pe/E-tRNA (structure II-D)
Method: EM (single particle) / Resolution: 3.1 Å

42577

8uua

EMDB-42577, PDB-8uua:
Cryo-EM structure of the Listeria innocua 50S ribosomal subunit in complex with HflXr (structure III)
Method: EM (single particle) / Resolution: 2.7 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-K:
Unknown entry

ChemComp-GCP:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-PCP, energy-carrying molecule analogue*YM

Source
  • listeria innocua (bacteria)
  • escherichia coli (E. coli)
  • escherichia phage t4 (virus)
  • listeria monocytogenes egd-e (bacteria)
  • listeria monocytogenes serovar 1/2a (strain atcc baa-679 / egd-e) (bacteria)
KeywordsRIBOSOME / cryo-EM / recycling / HPF / time-resolved / HflXr

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