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- EMDB-22469: 70S ribosome stalled on long mRNA with ArfB bound in the A site -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22469 | |||||||||
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Title | 70S ribosome stalled on long mRNA with ArfB bound in the A site | |||||||||
![]() | Refinement map of 3.5 Angstrom was blocfiltered with no B factor applied. | |||||||||
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Function / homology | ![]() translation release factor activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | 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 | ![]() | 15.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 69.4 KB 69.4 KB | Display Display | ![]() |
Images | ![]() | 188.4 KB | ||
Others | ![]() ![]() ![]() | 164.8 MB 83.8 MB 83.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jt2MC ![]() 7jssC ![]() 7jswC ![]() 7jszC ![]() 7jt1C ![]() 7jt3C C: citing same article ( M: atomic model generated by this map |
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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 | Refinement map of 3.5 Angstrom was blocfiltered with no B factor applied. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.042 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 3.5 Angstrom map with no B factor applied.
File | emd_22469_additional_1.map | ||||||||||||
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Annotation | Original 3.5 Angstrom map with no B factor applied. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_22469_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_22469_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : 70S ribosome stalled on long mRNA with ArfB bound in the A site
+Supramolecule #1: 70S ribosome stalled on long mRNA with ArfB bound in 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 L13
+Macromolecule #9: 50S ribosomal protein L14
+Macromolecule #10: 50S ribosomal protein L15
+Macromolecule #11: 50S ribosomal protein L16
+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 L32
+Macromolecule #26: 50S ribosomal protein L33
+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 #55: Peptidyl-tRNA hydrolase ArfB
+Macromolecule #50: 16S ribosomal RNA
+Macromolecule #51: 23S ribosomal RNA
+Macromolecule #52: 5S ribosomal RNA
+Macromolecule #53: tRNAfMet
+Macromolecule #54: mRNA
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 49.6 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER / Details: Ab initio |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8184 |