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Yorodumi- EMDB-21479: Class 2 from 3D classification of Bacillus subtilus delta HPF rib... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21479 | |||||||||
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Title | Class 2 from 3D classification of Bacillus subtilus delta HPF ribosomes | |||||||||
Map data | Class 2 from 3D classification of Bacillus subtilus delta HPF ribosomes | |||||||||
Sample |
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Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.31 Å | |||||||||
Authors | Feaga HA / Kopylov M / Jenny KK / Marko J / Dworkin J | |||||||||
Funding support | United States, 1 items
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Citation | Journal: J Bacteriol / Year: 2020 Title: Ribosome Dimerization Protects the Small Subunit. Authors: Heather A Feaga / Mykhailo Kopylov / Jenny Kim Kim / Marko Jovanovic / Jonathan Dworkin / Abstract: When nutrients become scarce, bacteria can enter an extended state of quiescence. A major challenge of this state is how to preserve ribosomes for the return to favorable conditions. Here, we show ...When nutrients become scarce, bacteria can enter an extended state of quiescence. A major challenge of this state is how to preserve ribosomes for the return to favorable conditions. Here, we show that the ribosome dimerization protein hibernation-promoting factor (HPF) functions to protect essential ribosomal proteins. Ribosomes isolated from strains lacking HPF (Δ) or encoding a mutant allele of HPF that binds the ribosome but does not mediate dimerization were substantially depleted of the small subunit proteins S2 and S3. Strikingly, these proteins are located directly at the ribosome dimer interface. We used single-particle cryo-electron microscopy (cryo-EM) to further characterize these ribosomes and observed that a high percentage of ribosomes were missing S2, S3, or both. These data support a model in which the ribosome dimerization activity of HPF evolved to protect labile proteins that are essential for ribosome function. HPF is almost universally conserved in bacteria, and HPF deletions in diverse species exhibit decreased viability during starvation. Our data provide mechanistic insight into this phenotype and establish a mechanism for how HPF protects ribosomes during quiescence. The formation of ribosome dimers during periods of dormancy is widespread among bacteria. Dimerization is typically mediated by a single protein, hibernation-promoting factor (HPF). Bacteria lacking HPF exhibit strong defects in viability and pathogenesis and, in some species, extreme loss of rRNA. The mechanistic basis of these phenotypes has not been determined. Here, we report that HPF from the Gram-positive bacterium preserves ribosomes by preventing the loss of essential ribosomal proteins at the dimer interface. This protection may explain phenotypes associated with the loss of HPF, since ribosome protection would aid survival during nutrient limitation and impart a strong selective advantage when the bacterial cell rapidly reinitiates growth in the presence of sufficient nutrients. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21479.map.gz | 13.8 MB | EMDB map data format | |
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Header (meta data) | emd-21479-v30.xml emd-21479.xml | 9 KB 9 KB | Display Display | EMDB header |
Images | emd_21479.png | 202.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21479 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21479 | HTTPS FTP |
-Validation report
Summary document | emd_21479_validation.pdf.gz | 77.7 KB | Display | EMDB validaton report |
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Full document | emd_21479_full_validation.pdf.gz | 76.8 KB | Display | |
Data in XML | emd_21479_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21479 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21479 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21479.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Class 2 from 3D classification of Bacillus subtilus delta HPF ribosomes | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.121 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Delta hpf 70S
Entire | Name: Delta hpf 70S |
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Components |
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-Supramolecule #1: Delta hpf 70S
Supramolecule | Name: Delta hpf 70S / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: UltrAuFoil / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 56.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20366 |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |