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- EMDB-43076: 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) (Composite structure 6) | ||||||||||||
![]() | Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP). Composite map | ||||||||||||
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![]() | cryo-EM / mycobacteria / hibernation / Msmeg1130 / Balon / MsmegEF-Tu / RIBOSOME | ||||||||||||
Function / homology | ![]() translation elongation factor activity / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...translation elongation factor activity / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
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. | ||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 416.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 83.8 KB 83.8 KB | Display Display | ![]() |
Images | ![]() | 172.5 KB | ||
Filedesc metadata | ![]() | 15.9 KB | ||
Others | ![]() ![]() | 416.5 MB 416.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8v9lMC ![]() 8rd8C ![]() 8rdvC ![]() 8rdwC ![]() 8v9jC ![]() 8v9kC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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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). Composite 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
-Half map: Mycobacterium smegmatis 70S ribosome in complex with hibernation...
File | emd_43076_half_map_1.map | ||||||||||||
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Annotation | Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP). Composite half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Mycobacterium smegmatis 70S ribosome in complex with hibernation...
File | emd_43076_half_map_2.map | ||||||||||||
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Annotation | Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP). Composite half-map 1 | ||||||||||||
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 ...
+Supramolecule #1: Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in ...
+Macromolecule #1: 16S Ribosomal RNA
+Macromolecule #22: poly-U mRNA
+Macromolecule #24: pe/E deacylated phenylanaline-tRNA
+Macromolecule #26: 23S Ribosomal RNA
+Macromolecule #27: 5S Ribosomal RNA
+Macromolecule #2: 30S Ribosomal Protein S2
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: 30S ribosomal protein S4
+Macromolecule #5: Small ribosomal subunit protein uS5
+Macromolecule #6: 30S ribosomal protein S6
+Macromolecule #7: 30S ribosomal protein S7
+Macromolecule #8: Small ribosomal subunit protein uS8
+Macromolecule #9: 30S ribosomal protein S9
+Macromolecule #10: 30S ribosomal protein S10
+Macromolecule #11: 30S ribosomal protein S11
+Macromolecule #12: 30S ribosomal protein S12
+Macromolecule #13: 30S ribosomal protein S13
+Macromolecule #14: Small ribosomal subunit protein uS14B
+Macromolecule #15: Small ribosomal subunit protein uS15
+Macromolecule #16: 30S ribosomal protein S16
+Macromolecule #17: 30S ribosomal protein S17
+Macromolecule #18: Small ribosomal subunit protein bS18B
+Macromolecule #19: 30S ribosomal protein S19
+Macromolecule #20: 30S ribosomal protein S20
+Macromolecule #21: 30S Ribosomal Protein S22
+Macromolecule #23: Elongation factor Tu
+Macromolecule #25: Ribosome hibernation factor Balon (MSMEG_1130)
+Macromolecule #28: 50S ribosomal protein L2
+Macromolecule #29: 50S ribosomal protein L3
+Macromolecule #30: Large ribosomal subunit protein uL4
+Macromolecule #31: Large ribosomal subunit protein uL5
+Macromolecule #32: 50S ribosomal protein L6
+Macromolecule #33: 50S ribosomal protein L9
+Macromolecule #34: 50S ribosomal protein L10
+Macromolecule #35: 50S ribosomal protein L11
+Macromolecule #36: Large ribosomal subunit protein uL13
+Macromolecule #37: 50S ribosomal protein L14
+Macromolecule #38: 50S ribosomal protein L15
+Macromolecule #39: Large ribosomal subunit protein uL16
+Macromolecule #40: 50S ribosomal protein L17
+Macromolecule #41: Large ribosomal subunit protein uL18
+Macromolecule #42: 50S ribosomal protein L19
+Macromolecule #43: Large ribosomal subunit protein bL20
+Macromolecule #44: Large ribosomal subunit protein bL21
+Macromolecule #45: Large ribosomal subunit protein uL22
+Macromolecule #46: Large ribosomal subunit protein uL23
+Macromolecule #47: 50S ribosomal protein L24
+Macromolecule #48: 50S ribosomal protein L25
+Macromolecule #49: 50S ribosomal protein L27
+Macromolecule #50: Large ribosomal subunit protein bL28
+Macromolecule #51: 50S ribosomal protein L29
+Macromolecule #52: 50S ribosomal protein L30
+Macromolecule #53: Large ribosomal subunit protein bL31
+Macromolecule #54: 50S ribosomal protein L32
+Macromolecule #55: Large ribosomal subunit protein bL33A
+Macromolecule #56: 50S ribosomal protein L34
+Macromolecule #57: 50S ribosomal protein L35
+Macromolecule #58: 50S ribosomal protein L36
+Macromolecule #59: 50S Ribosomal Protein L27
+Macromolecule #60: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #61: ZINC ION
-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
-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 |
Output model | ![]() PDB-8v9l: |