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- EMDB-43077: Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in ... -
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Open data
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Basic information
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Title | Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP) (Structure 6) | ||||||||||||
![]() | Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP). Map | ||||||||||||
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![]() | cryo-EM / mycobacteria / hibernation / Msmeg1130 / Balon / MsmegEF-Tu / RIBOSOME | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | ||||||||||||
![]() | Rybak MY / Helena-Bueno K / Hill CH / Melnikov SV / Gagnon MG | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A new family of bacterial ribosome hibernation factors. Authors: Karla Helena-Bueno / Mariia Yu Rybak / Chinenye L Ekemezie / Rudi Sullivan / Charlotte R Brown / Charlotte Dingwall / Arnaud Baslé / Claudia Schneider / James P R Connolly / James N Blaza / ...Authors: Karla Helena-Bueno / Mariia Yu Rybak / Chinenye L Ekemezie / Rudi Sullivan / Charlotte R Brown / Charlotte Dingwall / Arnaud Baslé / Claudia Schneider / James P R Connolly / James N Blaza / Bálint Csörgő / Patrick J Moynihan / Matthieu G Gagnon / Chris H Hill / Sergey V Melnikov / ![]() ![]() ![]() Abstract: To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage. In bacteria, two families of ...To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage. In bacteria, two families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats and environmental stressors have confounded their discovery. Here, by combining cryogenic electron microscopy, genetics and biochemistry, we identify Balon, a new hibernation factor in the cold-adapted bacterium Psychrobacter urativorans. We show that Balon is a distant homologue of the archaeo-eukaryotic translation factor aeRF1 and is found in 20% of representative bacteria. During cold shock or stationary phase, Balon occupies the ribosomal A site in both vacant and actively translating ribosomes in complex with EF-Tu, highlighting an unexpected role for EF-Tu in the cellular stress response. Unlike typical A-site substrates, Balon binds to ribosomes in an mRNA-independent manner, initiating a new mode of ribosome hibernation that can commence while ribosomes are still engaged in protein synthesis. Our work suggests that Balon-EF-Tu-regulated ribosome hibernation is a ubiquitous bacterial stress-response mechanism, and we demonstrate that putative Balon homologues in Mycobacteria bind to ribosomes in a similar fashion. This finding calls for a revision of the current model of ribosome hibernation inferred from common model organisms and holds numerous implications for how we understand and study ribosome hibernation. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 257.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.2 KB 19.2 KB | Display Display | ![]() |
Images | ![]() | 172.5 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Filedesc metadata | ![]() | 4.8 KB | ||
Others | ![]() ![]() ![]() | 415.1 MB 475.7 MB 475.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP). Map | ||||||||||||||||||||
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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Density Histograms |
-Additional map: Mycobacterium smegmatis 70S ribosome in complex with hibernation...
File | emd_43077_additional_1.map | ||||||||||||
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Annotation | Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP). Sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Mycobacterium smegmatis 70S ribosome in complex with hibernation...
File | emd_43077_half_map_1.map | ||||||||||||
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Annotation | Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP). Half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Mycobacterium smegmatis 70S ribosome in complex with hibernation...
File | emd_43077_half_map_2.map | ||||||||||||
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Annotation | Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP). Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in ...
Entire | Name: Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP) (Structure 6) |
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Components |
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-Supramolecule #1: Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in ...
Supramolecule | Name: Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP) (Structure 6) type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 2.6 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: 7.5 Details: 20 mM HEPES-KOH, 60 mM KCl, 10 mM MgCl2, 1 mM dithiothreitol |
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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: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 10161 / Average electron dose: 40.12 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: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
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
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 101909 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1) |
-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 |