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- EMDB-42568: Focus refined map of the swiveled head domain of the 30S subunit ... -
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Open data
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Basic information
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Title | 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) | |||||||||||||||
![]() | Focus refined map of Listeria innocua 30S head from Structure II-C | |||||||||||||||
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![]() | cryo-EM / recycling / HflXr / time-resolved / RIBOSOME | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||
![]() | Seely SM / Basu RS / Gagnon MG | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanistic insights into the alternative ribosome recycling by HflXr. Authors: Savannah M Seely / Ritwika S Basu / Matthieu G Gagnon / ![]() Abstract: 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 ...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. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 253.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.5 KB 26.5 KB | Display Display | ![]() |
Images | ![]() | 185.2 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Filedesc metadata | ![]() | 4.7 KB | ||
Others | ![]() ![]() ![]() | 483.3 MB 475.6 MB 475.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Focus refined map of Listeria innocua 30S head from Structure II-C | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Focus refined map of Listeria innocua 30S head...
File | emd_42568_additional_1.map | ||||||||||||
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Annotation | Focus refined map of Listeria innocua 30S head from Structure II-C (Sharpened map) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Focus refined map of Listeria innocua 30S head...
File | emd_42568_half_map_1.map | ||||||||||||
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Annotation | Focus refined map of Listeria innocua 30S head from Structure II-C (Half map) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Focus refined map of Listeria innocua 30S head...
File | emd_42568_half_map_2.map | ||||||||||||
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Annotation | Focus refined map of Listeria innocua 30S head from Structure II-C (Half map) | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Listeria innocua 70S ribosome in complex with HflXr and pe/E-tRNA
Entire | Name: Listeria innocua 70S ribosome in complex with HflXr and pe/E-tRNA |
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Components |
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-Supramolecule #1: Listeria innocua 70S ribosome in complex with HflXr and pe/E-tRNA
Supramolecule | Name: Listeria innocua 70S ribosome in complex with HflXr and pe/E-tRNA type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#54 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 2.5 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.6 |
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 295 K / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 10151 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 96000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |