+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21857 | |||||||||||||||
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Title | 70S ribosome without free 5S rRNA and with a perturbed PTC | |||||||||||||||
Map data | Cryo-EM map of vacant 70S ribosome with 23S-cp5s rRNA and abberant PTC | |||||||||||||||
Sample |
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Keywords | Ribosome / 23S-cp5S rRNA / engineering | |||||||||||||||
Function / homology | Function and homology information negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / 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 / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | Escherichia coli (E. coli) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
Authors | Loveland AB / Korostelev AA | |||||||||||||||
Funding support | United States, Estonia, 4 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Ribosome engineering reveals the importance of 5S rRNA autonomy for ribosome assembly. Authors: Shijie Huang / Nikolay A Aleksashin / Anna B Loveland / Dorota Klepacki / Kaspar Reier / Amira Kefi / Teresa Szal / Jaanus Remme / Luc Jaeger / Nora Vázquez-Laslop / Andrei A Korostelev / Alexander S Mankin / Abstract: 5S rRNA is an indispensable component of cytoplasmic ribosomes in all species. The functions of 5S rRNA and the reasons for its evolutionary preservation as an independent molecule remain unclear. ...5S rRNA is an indispensable component of cytoplasmic ribosomes in all species. The functions of 5S rRNA and the reasons for its evolutionary preservation as an independent molecule remain unclear. Here we used ribosome engineering to investigate whether 5S rRNA autonomy is critical for ribosome function and cell survival. By linking circularly permutated 5S rRNA with 23S rRNA we generated a bacterial strain devoid of free 5S rRNA. Viability of the engineered cells demonstrates that autonomous 5S rRNA is dispensable for cell growth under standard conditions and is unlikely to have essential functions outside the ribosome. The fully assembled ribosomes carrying 23S-5S rRNA are highly active in translation. However, the engineered cells accumulate aberrant 50S subunits unable to form stable 70S ribosomes. Cryo-EM analysis revealed a malformed peptidyl transferase center in the misassembled 50S subunits. Our results argue that the autonomy of 5S rRNA is preserved due to its role in ribosome biogenesis. | |||||||||||||||
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_21857.map.gz | 794.7 MB | EMDB map data format | |
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Header (meta data) | emd-21857-v30.xml emd-21857.xml | 73.6 KB 73.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21857_fsc.xml | 20.7 KB | Display | FSC data file |
Images | emd_21857.png | 175.8 KB | ||
Filedesc metadata | emd-21857.cif.gz | 13.4 KB | ||
Others | emd_21857_additional.map.gz emd_21857_half_map_1.map.gz emd_21857_half_map_2.map.gz | 794.9 MB 122.7 MB 122.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21857 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21857 | HTTPS FTP |
-Validation report
Summary document | emd_21857_validation.pdf.gz | 958.4 KB | Display | EMDB validaton report |
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Full document | emd_21857_full_validation.pdf.gz | 957.9 KB | Display | |
Data in XML | emd_21857_validation.xml.gz | 30.1 KB | Display | |
Data in CIF | emd_21857_validation.cif.gz | 39.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21857 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21857 | HTTPS FTP |
-Related structure data
Related structure data | 6wnvMC 6wntC 6wnwC C: citing same article (ref.) M: atomic model generated by this map |
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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_21857.map.gz / Format: CCP4 / Size: 857.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of vacant 70S ribosome with 23S-cp5s rRNA and abberant PTC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Cryo-EM map with B-factor filtering of vacant 70S...
File | emd_21857_additional.map | ||||||||||||
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Annotation | Cryo-EM map with B-factor filtering of vacant 70S ribosome with 23S-cp5s rRNA and abberant PTC | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM half map of vacant 70S ribosome with...
File | emd_21857_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM half map of vacant 70S ribosome with 23S-cp5s rRNA and abberant PTC | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM half map of vacant 70S ribosome with...
File | emd_21857_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM half map of vacant 70S ribosome with 23S-cp5s rRNA and abberant PTC | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 70S ribosome without free 5S rRNA and with perturbed PTC
+Supramolecule #1: 70S ribosome without free 5S rRNA and with perturbed PTC
+Macromolecule #1: 50S ribosomal protein L2
+Macromolecule #2: 50S ribosomal protein L3
+Macromolecule #3: 50S ribosomal protein L4
+Macromolecule #4: 50S ribosomal protein L5
+Macromolecule #5: 50S ribosomal protein L6
+Macromolecule #6: 50S ribosomal protein L9
+Macromolecule #7: 50S ribosomal protein L10
+Macromolecule #8: 50S ribosomal protein L11
+Macromolecule #9: 50S ribosomal protein L13
+Macromolecule #10: 50S ribosomal protein L14
+Macromolecule #11: 50S ribosomal protein L15
+Macromolecule #12: 50S ribosomal protein L17
+Macromolecule #13: 50S ribosomal protein L18
+Macromolecule #14: 50S ribosomal protein L19
+Macromolecule #15: 50S ribosomal protein L20
+Macromolecule #16: 50S ribosomal protein L21
+Macromolecule #17: 50S ribosomal protein L22
+Macromolecule #18: 50S ribosomal protein L23
+Macromolecule #19: 50S ribosomal protein L24
+Macromolecule #20: 50S ribosomal protein L25
+Macromolecule #21: 50S ribosomal protein L27
+Macromolecule #22: 50S ribosomal protein L28
+Macromolecule #23: 50S ribosomal protein L29
+Macromolecule #24: 50S ribosomal protein L30
+Macromolecule #25: 50S ribosomal protein L31
+Macromolecule #26: 50S ribosomal protein L32
+Macromolecule #27: 50S ribosomal protein L34
+Macromolecule #28: 50S ribosomal protein L35
+Macromolecule #29: 50S ribosomal protein L36
+Macromolecule #30: 30S ribosomal protein S2
+Macromolecule #31: 30S ribosomal protein S3
+Macromolecule #32: 30S ribosomal protein S4
+Macromolecule #33: 30S ribosomal protein S5
+Macromolecule #34: 30S ribosomal protein S6
+Macromolecule #35: 30S ribosomal protein S7
+Macromolecule #36: 30S ribosomal protein S8
+Macromolecule #37: 30S ribosomal protein S9
+Macromolecule #38: 30S ribosomal protein S10
+Macromolecule #39: 30S ribosomal protein S11
+Macromolecule #40: 30S ribosomal protein S12
+Macromolecule #41: 30S ribosomal protein S13
+Macromolecule #42: 30S ribosomal protein S14
+Macromolecule #43: 30S ribosomal protein S15
+Macromolecule #44: 30S ribosomal protein S16
+Macromolecule #45: 30S ribosomal protein S17
+Macromolecule #46: 30S ribosomal protein S18
+Macromolecule #47: 30S ribosomal protein S19
+Macromolecule #48: 30S ribosomal protein S20
+Macromolecule #49: 30S ribosomal protein S21
+Macromolecule #50: 50S ribosomal protein L1
+Macromolecule #51: 16S ribosomal RNA
+Macromolecule #52: 23s-5s joint ribosomal RNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | .1 mg/mL |
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Buffer | pH: 7 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS TALOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |