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Yorodumi- EMDB-42566: Cryo-EM structure of the Listeria innocua 70S ribosome in complex... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42566 | |||||||||||||||
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Title | Cryo-EM structure of the Listeria innocua 70S ribosome in complex with HflXr, HPF, and E-site tRNA (structure II-B) | |||||||||||||||
Map data | Composite Cryo-EM map of the Listeria innocua 70S ribosome in complex with HflXr, HPF, and E-site tRNA (structure II-B) | |||||||||||||||
Sample |
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Keywords | cryo-EM / recycling / HflXr / HPF / time-resolved / RIBOSOME | |||||||||||||||
Function / homology | Function and homology information negative regulation of translational elongation / ribosomal small subunit binding / large ribosomal subunit / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding ...negative regulation of translational elongation / ribosomal small subunit binding / large ribosomal subunit / ribosome binding / 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 / tRNA binding / cytoplasmic translation / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | Listeria innocua (bacteria) / Escherichia coli (E. coli) / Listeria monocytogenes EGD-e (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||
Authors | Seely SM / Basu RS / Gagnon MG | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Nucleic Acids Res / Year: 2024 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 | emd_42566.map.gz | 251 MB | EMDB map data format | |
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Header (meta data) | emd-42566-v30.xml emd-42566.xml | 76.5 KB 76.5 KB | Display Display | EMDB header |
Images | emd_42566.png | 155.9 KB | ||
Filedesc metadata | emd-42566.cif.gz | 14.5 KB | ||
Others | emd_42566_half_map_1.map.gz emd_42566_half_map_2.map.gz | 250.8 MB 250.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42566 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42566 | HTTPS FTP |
-Validation report
Summary document | emd_42566_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_42566_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_42566_validation.xml.gz | 19 KB | Display | |
Data in CIF | emd_42566_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42566 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42566 | HTTPS FTP |
-Related structure data
Related structure data | 8uu7MC 8uu4C 8uu5C 8uu6C 8uu8C 8uu9C 8uuaC C: citing same article (ref.) M: atomic model generated by this map |
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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_42566.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Composite Cryo-EM map of the Listeria innocua 70S ribosome in complex with HflXr, HPF, and E-site tRNA (structure II-B) | ||||||||||||||||||||
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: Listeria innocua 70S ribosome in complex with HflXr,...
File | emd_42566_half_map_1.map | ||||||||||||
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Annotation | Listeria innocua 70S ribosome in complex with HflXr, HPF, and E-site tRNA (structure II-B) Composite half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Listeria innocua 70S ribosome in complex with HflXr,...
File | emd_42566_half_map_2.map | ||||||||||||
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Annotation | Listeria innocua 70S ribosome in complex with HflXr, HPF, and E-site tRNA (structure II-B) Composite half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Listeria innocua 70S ribosome in complex with HPF, HflXr and E-si...
+Supramolecule #1: Listeria innocua 70S ribosome in complex with HPF, HflXr and E-si...
+Macromolecule #1: 16S Ribosomal RNA
+Macromolecule #21: E-site Phenylalanine tRNA
+Macromolecule #24: 23S Ribosomal RNA
+Macromolecule #25: 5S Ribosomal RNA
+Macromolecule #2: Small ribosomal subunit protein uS2
+Macromolecule #3: Small ribosomal subunit protein uS3
+Macromolecule #4: Small ribosomal subunit protein uS4
+Macromolecule #5: Small ribosomal subunit protein uS5
+Macromolecule #6: Small ribosomal subunit protein bS6
+Macromolecule #7: Small ribosomal subunit protein uS7
+Macromolecule #8: Small ribosomal subunit protein uS8
+Macromolecule #9: Small ribosomal subunit protein uS9
+Macromolecule #10: Small ribosomal subunit protein uS10
+Macromolecule #11: Small ribosomal subunit protein uS11
+Macromolecule #12: Small ribosomal subunit protein uS12
+Macromolecule #13: Small ribosomal subunit protein uS13
+Macromolecule #14: Small ribosomal subunit protein uS14
+Macromolecule #15: Small ribosomal subunit protein uS15
+Macromolecule #16: Small ribosomal subunit protein bS16
+Macromolecule #17: Small ribosomal subunit protein uS17
+Macromolecule #18: Small ribosomal subunit protein bS18
+Macromolecule #19: Small ribosomal subunit protein uS19
+Macromolecule #20: Small ribosomal subunit protein bS20
+Macromolecule #22: GTPase HflX
+Macromolecule #23: Ribosome hibernation promoting factor
+Macromolecule #26: Large ribosomal subunit protein uL2
+Macromolecule #27: Large ribosomal subunit protein uL3
+Macromolecule #28: Large ribosomal subunit protein uL4
+Macromolecule #29: Large ribosomal subunit protein uL5
+Macromolecule #30: Large ribosomal subunit protein uL6
+Macromolecule #31: Large ribosomal subunit protein uL13
+Macromolecule #32: Large ribosomal subunit protein uL14
+Macromolecule #33: Large ribosomal subunit protein uL15
+Macromolecule #34: Large ribosomal subunit protein uL16
+Macromolecule #35: Large ribosomal subunit protein bL17
+Macromolecule #36: Large ribosomal subunit protein uL18
+Macromolecule #37: Large ribosomal subunit protein bL19
+Macromolecule #38: Large ribosomal subunit protein bL20
+Macromolecule #39: Large ribosomal subunit protein bL21
+Macromolecule #40: Large ribosomal subunit protein uL22
+Macromolecule #41: Large ribosomal subunit protein uL23
+Macromolecule #42: Large ribosomal subunit protein uL24
+Macromolecule #43: Large ribosomal subunit protein bL27
+Macromolecule #44: Large ribosomal subunit protein bL28
+Macromolecule #45: Large ribosomal subunit protein uL29
+Macromolecule #46: Large ribosomal subunit protein uL30
+Macromolecule #47: Large ribosomal subunit protein bL31B
+Macromolecule #48: Large ribosomal subunit protein bL32
+Macromolecule #49: Large ribosomal subunit protein bL33
+Macromolecule #50: Large ribosomal subunit protein bL34
+Macromolecule #51: Large ribosomal subunit protein bL35
+Macromolecule #52: Large ribosomal subunit protein bL36
+Macromolecule #53: MAGNESIUM ION
+Macromolecule #54: ZINC ION
+Macromolecule #55: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
+Macromolecule #56: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-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: FIELD EMISSION GUN |
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 |