[English] 日本語
![](img/lk-miru.gif)
- EMDB-10353: Release factor-dependent ribosome rescue by BrfA in the Gram-posi... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-10353 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | Cryo-EM / bacterial ribosome rescue / Bacillus ribosome rescue factor A / Bacillus subtilis peptide chain release factor 2 / RIBOSOME | |||||||||
Function / homology | ![]() translation release factor activity, codon specific / negative regulation of cytoplasmic translational initiation / 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 ...translation release factor activity, codon specific / negative regulation of cytoplasmic translational initiation / 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 / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.06 Å | |||||||||
![]() | Muller C / Beckert B | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis. Authors: Naomi Shimokawa-Chiba / Claudia Müller / Keigo Fujiwara / Bertrand Beckert / Koreaki Ito / Daniel N Wilson / Shinobu Chiba / ![]() ![]() Abstract: Rescue of the ribosomes from dead-end translation complexes, such as those on truncated (non-stop) mRNA, is essential for the cell. Whereas bacteria use trans-translation for ribosome rescue, some ...Rescue of the ribosomes from dead-end translation complexes, such as those on truncated (non-stop) mRNA, is essential for the cell. Whereas bacteria use trans-translation for ribosome rescue, some Gram-negative species possess alternative and release factor (RF)-dependent rescue factors, which enable an RF to catalyze stop-codon-independent polypeptide release. We now discover that the Gram-positive Bacillus subtilis has an evolutionarily distinct ribosome rescue factor named BrfA. Genetic analysis shows that B. subtilis requires the function of either trans-translation or BrfA for growth, even in the absence of proteotoxic stresses. Biochemical and cryo-electron microscopy (cryo-EM) characterization demonstrates that BrfA binds to non-stop stalled ribosomes, recruits homologous RF2, but not RF1, and induces its transition into an open active conformation. Although BrfA is distinct from E. coli ArfA, they use convergent strategies in terms of mode of action and expression regulation, indicating that many bacteria may have evolved as yet unidentified ribosome rescue systems. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 20 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 85.5 KB 85.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.1 KB | Display | ![]() |
Images | ![]() | 40.2 KB | ||
Filedesc metadata | ![]() | 14.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6szsMC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
+Entire : E. coli 70S stalled on truncated mRNA in complex BsBrfA and BsRF2...
+Supramolecule #1: E. coli 70S stalled on truncated mRNA in complex BsBrfA and BsRF2...
+Supramolecule #2: Escherichia coli ribosome with P-site tRNA-Pro(CGG, carrying the ...
+Supramolecule #3: Bacillus subtilis ribosome rescue factor (BrfA; former YqkK) and ...
+Macromolecule #1: 50S ribosomal protein L32
+Macromolecule #2: 50S ribosomal protein L33
+Macromolecule #3: 50S ribosomal protein L34
+Macromolecule #4: 50S ribosomal protein L35
+Macromolecule #5: 50S ribosomal protein L36
+Macromolecule #6: 50S ribosomal protein L31
+Macromolecule #9: 50S ribosomal protein L2
+Macromolecule #10: 50S ribosomal protein L3
+Macromolecule #11: 50S ribosomal protein L4
+Macromolecule #12: 50S ribosomal protein L5
+Macromolecule #13: 50S ribosomal protein L6
+Macromolecule #14: 50S ribosomal protein L9
+Macromolecule #15: 50S ribosomal protein L13
+Macromolecule #16: 50S ribosomal protein L14
+Macromolecule #17: 50S ribosomal protein L15
+Macromolecule #18: 50S ribosomal protein L16
+Macromolecule #19: 50S ribosomal protein L17
+Macromolecule #20: 50S ribosomal protein L18
+Macromolecule #21: 50S ribosomal protein L19
+Macromolecule #22: 50S ribosomal protein L20
+Macromolecule #23: 50S ribosomal protein L21
+Macromolecule #24: 50S ribosomal protein L22
+Macromolecule #25: 50S ribosomal protein L23
+Macromolecule #26: 50S ribosomal protein L24
+Macromolecule #27: 50S ribosomal protein L25
+Macromolecule #28: 50S ribosomal protein L27
+Macromolecule #29: 50S ribosomal protein L28
+Macromolecule #30: 50S ribosomal protein L29
+Macromolecule #31: 50S ribosomal protein L30
+Macromolecule #33: 30S ribosomal protein S2
+Macromolecule #34: 30S ribosomal protein S3
+Macromolecule #35: 30S ribosomal protein S4
+Macromolecule #36: 30S ribosomal protein S5
+Macromolecule #37: 30S ribosomal protein S6
+Macromolecule #38: 30S ribosomal protein S7
+Macromolecule #39: 30S ribosomal protein S8
+Macromolecule #40: 30S ribosomal protein S9
+Macromolecule #41: 30S ribosomal protein S10
+Macromolecule #42: 30S ribosomal protein S11
+Macromolecule #43: 30S ribosomal protein S12
+Macromolecule #44: 30S ribosomal protein S13
+Macromolecule #45: 30S ribosomal protein S14
+Macromolecule #46: 30S ribosomal protein S15
+Macromolecule #47: 30S ribosomal protein S16
+Macromolecule #48: 30S ribosomal protein S17
+Macromolecule #49: 30S ribosomal protein S18
+Macromolecule #50: 30S ribosomal protein S19
+Macromolecule #51: 30S ribosomal protein S20
+Macromolecule #52: 30S ribosomal protein S21
+Macromolecule #55: Uncharacterized protein YqkK
+Macromolecule #56: Peptide chain release factor 2
+Macromolecule #7: 23S ribosomal RNA
+Macromolecule #8: 5S ribosomal RNA
+Macromolecule #32: 16S ribosomal RNA
+Macromolecule #53: mRNA
+Macromolecule #54: P-site tRNA-Pro(CGG)
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.2 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 83.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |