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- EMDB-22464: ArfB Rescue of a 70S Ribosome stalled on truncated mRNA with a pa... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22464 | |||||||||
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Title | ArfB Rescue of a 70S Ribosome stalled on truncated mRNA with a partial A-site codon (+2-IV) | |||||||||
![]() | Map used in refinement. Map was blocfiltered and no B factor was applied. | |||||||||
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![]() | Ribosome / ArfB / mRNA / TRANSLATION / RIBOSOME-TRANSLATION complex | |||||||||
Function / homology | ![]() translation release factor activity / peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding ...translation release factor activity / peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / stringent response / mRNA base-pairing translational repressor activity / 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 / translational termination / DnaA-L2 complex / four-way junction DNA binding / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / rescue of stalled ribosome / ribosome assembly / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / DNA endonuclease activity / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ribosomal large subunit assembly / 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 / tRNA binding / cytoplasmic translation / 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 | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Carbone CE / Korostelev AA | |||||||||
Funding support | ![]()
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![]() | ![]() Title: ArfB can displace mRNA to rescue stalled ribosomes. Authors: Christine E Carbone / Gabriel Demo / Rohini Madireddy / Egor Svidritskiy / Andrei A Korostelev / ![]() ![]() Abstract: Ribosomes stalled during translation must be rescued to replenish the pool of translation-competent ribosomal subunits. Bacterial alternative rescue factor B (ArfB) releases nascent peptides from ...Ribosomes stalled during translation must be rescued to replenish the pool of translation-competent ribosomal subunits. Bacterial alternative rescue factor B (ArfB) releases nascent peptides from ribosomes stalled on mRNAs truncated at the A site, allowing ribosome recycling. Prior structural work revealed that ArfB recognizes such ribosomes by inserting its C-terminal α-helix into the vacant mRNA tunnel. In this work, we report that ArfB can efficiently recognize a wider range of mRNA substrates, including longer mRNAs that extend beyond the A-site codon. Single-particle cryo-EM unveils that ArfB employs two modes of function depending on the mRNA length. ArfB acts as a monomer to accommodate a shorter mRNA in the ribosomal A site. By contrast, longer mRNAs are displaced from the mRNA tunnel by more than 20 Å and are stabilized in the intersubunit space by dimeric ArfB. Uncovering distinct modes of ArfB function resolves conflicting biochemical and structural studies, and may lead to re-examination of other ribosome rescue pathways, whose functions depend on mRNA lengths. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 25.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 75.4 KB 75.4 KB | Display Display | ![]() |
Images | ![]() | 105.9 KB | ||
Filedesc metadata | ![]() | 13.5 KB | ||
Others | ![]() ![]() ![]() | 317.4 MB 144 MB 144.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 853.4 KB | Display | ![]() |
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Full document | ![]() | 852.9 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jszMC ![]() 7jssC ![]() 7jswC ![]() 7jt1C ![]() 7jt2C ![]() 7jt3C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map used in refinement. Map was blocfiltered and no B factor was applied. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: Original 3.7 angstrom map with no B factor applied.
File | emd_22464_additional_1.map | ||||||||||||
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Annotation | Original 3.7 angstrom map with no B factor applied. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: First half map.
File | emd_22464_half_map_1.map | ||||||||||||
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Annotation | First half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Second half map.
File | emd_22464_half_map_2.map | ||||||||||||
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Annotation | Second half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : 70S ribosome stalled on truncated mRNA with ArfB bound to the A site.
+Supramolecule #1: 70S ribosome stalled on truncated mRNA with ArfB bound to the A site.
+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 L16
+Macromolecule #13: 50S ribosomal protein L17
+Macromolecule #14: 50S ribosomal protein L18
+Macromolecule #15: 50S ribosomal protein L19
+Macromolecule #16: 50S ribosomal protein L20
+Macromolecule #17: 50S ribosomal protein L21
+Macromolecule #18: 50S ribosomal protein L22
+Macromolecule #19: 50S ribosomal protein L23
+Macromolecule #20: 50S ribosomal protein L24
+Macromolecule #21: 50S ribosomal protein L25
+Macromolecule #22: 50S ribosomal protein L27
+Macromolecule #23: 50S ribosomal protein L28
+Macromolecule #24: 50S ribosomal protein L29
+Macromolecule #25: 50S ribosomal protein L30
+Macromolecule #26: 50S ribosomal protein L32
+Macromolecule #27: 50S ribosomal protein L33
+Macromolecule #28: 50S ribosomal protein L34
+Macromolecule #29: 50S ribosomal protein L35
+Macromolecule #30: 50S ribosomal protein L36
+Macromolecule #31: 30S ribosomal protein S2
+Macromolecule #32: 30S ribosomal protein S3
+Macromolecule #33: 30S ribosomal protein S4
+Macromolecule #34: 30S ribosomal protein S5
+Macromolecule #35: 30S ribosomal protein S6
+Macromolecule #36: 30S ribosomal protein S7
+Macromolecule #37: 30S ribosomal protein S8
+Macromolecule #38: 30S ribosomal protein S9
+Macromolecule #39: 30S ribosomal protein S10
+Macromolecule #40: 30S ribosomal protein S11
+Macromolecule #41: 30S ribosomal protein S12
+Macromolecule #42: 30S ribosomal protein S13
+Macromolecule #43: 30S ribosomal protein S14
+Macromolecule #44: 30S ribosomal protein S15
+Macromolecule #45: 30S ribosomal protein S16
+Macromolecule #46: 30S ribosomal protein S17
+Macromolecule #47: 30S ribosomal protein S18
+Macromolecule #48: 30S ribosomal protein S19
+Macromolecule #49: 30S ribosomal protein S20
+Macromolecule #50: 30S ribosomal protein S21
+Macromolecule #51: 50S ribosomal protein L1
+Macromolecule #57: Peptidyl-tRNA hydrolase ArfB
+Macromolecule #52: 16S ribosomal RNA
+Macromolecule #53: 23S ribosomal RNA
+Macromolecule #54: 5S ribosomal RNA
+Macromolecule #55: tRNAfMet
+Macromolecule #56: mRNA
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.5 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER / Details: Ab initio |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12528 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |