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Yorodumi- EMDB-19067: Cryo-EM structure of P. urativorans 70S ribosome in complex with ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19067 | |||||||||
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Title | Cryo-EM structure of P. urativorans 70S ribosome in complex with hibernation factors Balon and RaiA (structure 1). | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Ribosome / Hibernation factor / Dormancy / Balon | |||||||||
Function / homology | Function and homology information primary metabolic process / guanosine tetraphosphate binding / translation elongation factor activity / ribosomal small subunit biogenesis / large ribosomal subunit / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit ...primary metabolic process / guanosine tetraphosphate binding / translation elongation factor activity / ribosomal small subunit biogenesis / large ribosomal subunit / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / GTP binding / RNA binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Psychrobacter urativorans (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.62 Å | |||||||||
Authors | Helena-Bueno K / Rybak MY / Gagnon MG / Hill CH / Melnikov SV | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nature / Year: 2024 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 | emd_19067.map.gz | 352.4 MB | EMDB map data format | |
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Header (meta data) | emd-19067-v30.xml emd-19067.xml | 71.8 KB 71.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19067_fsc.xml | 19.1 KB | Display | FSC data file |
Images | emd_19067.png | 143.4 KB | ||
Masks | emd_19067_msk_1.map | 600.7 MB | Mask map | |
Filedesc metadata | emd-19067.cif.gz | 14.4 KB | ||
Others | emd_19067_half_map_1.map.gz emd_19067_half_map_2.map.gz | 483.2 MB 483.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19067 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19067 | HTTPS FTP |
-Validation report
Summary document | emd_19067_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_19067_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_19067_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | emd_19067_validation.cif.gz | 36.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19067 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19067 | HTTPS FTP |
-Related structure data
Related structure data | 8rd8MC 8rdvC 8rdwC 8v9jC 8v9kC 8v9lC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_19067.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.723 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19067_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19067_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19067_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Ribosomes isolated from ice-treated cultures of Psychrobacter ura...
+Supramolecule #1: Ribosomes isolated from ice-treated cultures of Psychrobacter ura...
+Macromolecule #1: Methyl-accepting chemotaxis protein
+Macromolecule #2: Small ribosomal subunit protein uS9
+Macromolecule #3: Elongation factor Tu
+Macromolecule #4: Large ribosomal subunit protein bL9
+Macromolecule #6: Small ribosomal subunit protein bS18
+Macromolecule #7: Small ribosomal subunit protein uS2
+Macromolecule #8: Small ribosomal subunit protein uS5
+Macromolecule #9: Small ribosomal subunit protein uS12
+Macromolecule #10: Large ribosomal subunit protein uL5
+Macromolecule #12: Large ribosomal subunit protein uL4
+Macromolecule #13: Large ribosomal subunit protein bL32
+Macromolecule #14: Large ribosomal subunit protein bL17
+Macromolecule #15: Large ribosomal subunit protein bL25
+Macromolecule #16: Large ribosomal subunit protein bL28
+Macromolecule #17: Large ribosomal subunit protein uL29
+Macromolecule #18: Large ribosomal subunit protein uL22
+Macromolecule #19: Small ribosomal subunit protein bS6
+Macromolecule #20: Large ribosomal subunit protein bL27
+Macromolecule #21: Large ribosomal subunit protein uL24
+Macromolecule #22: Large ribosomal subunit protein bL31B
+Macromolecule #23: Small ribosomal subunit protein uS14
+Macromolecule #24: Small ribosomal subunit protein uS15
+Macromolecule #25: Small ribosomal subunit protein uS13
+Macromolecule #27: Large ribosomal subunit protein bL20
+Macromolecule #28: Small ribosomal subunit protein uS19
+Macromolecule #29: Small ribosomal subunit protein uS8
+Macromolecule #30: Large ribosomal subunit protein uL6
+Macromolecule #31: Small ribosomal subunit protein uS7
+Macromolecule #32: Small ribosomal subunit protein uS3
+Macromolecule #33: Small ribosomal subunit protein uS11
+Macromolecule #34: Small ribosomal subunit protein bS21
+Macromolecule #35: Large ribosomal subunit protein uL30
+Macromolecule #36: Large ribosomal subunit protein uL13
+Macromolecule #37: Small ribosomal subunit protein uS10
+Macromolecule #38: Small ribosomal subunit protein uS17
+Macromolecule #39: Large ribosomal subunit protein bL34
+Macromolecule #40: Large ribosomal subunit protein bL21
+Macromolecule #41: Large ribosomal subunit protein uL18
+Macromolecule #42: Large ribosomal subunit protein uL15
+Macromolecule #43: Large ribosomal subunit protein uL14
+Macromolecule #44: Large ribosomal subunit protein uL3
+Macromolecule #45: Large ribosomal subunit protein uL16
+Macromolecule #46: Large ribosomal subunit protein bL35
+Macromolecule #47: Large ribosomal subunit protein bL19
+Macromolecule #48: Small ribosomal subunit protein bS16
+Macromolecule #49: Large ribosomal subunit protein bL33
+Macromolecule #50: Large ribosomal subunit protein uL2
+Macromolecule #51: Small ribosomal subunit protein uS4
+Macromolecule #52: Large ribosomal subunit protein uL23
+Macromolecule #53: Small ribosomal subunit protein bS20
+Macromolecule #54: Large ribosomal subunit protein bL36
+Macromolecule #55: 30S ribosomal protein S30
+Macromolecule #5: 23S rRNA
+Macromolecule #11: 5S rRNA
+Macromolecule #26: 16S rRNA
+Macromolecule #56: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.75 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |