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- PDB-7jsz: ArfB Rescue of a 70S Ribosome stalled on truncated mRNA with a pa... -
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Basic information
Entry | Database: PDB / ID: 7jsz | |||||||||
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Title | ArfB Rescue of a 70S Ribosome stalled on truncated mRNA with a partial A-site codon (+2-IV) | |||||||||
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![]() | RIBOSOME/TRANSLATION / Ribosome / ArfB / mRNA / TRANSLATION / RIBOSOME-TRANSLATION complex | |||||||||
Function / homology | ![]() translation release factor activity / peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation ...translation release factor activity / peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / 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 / rescue of stalled ribosome / 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 / 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 | ![]() ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Carbone, C.E. / Korostelev, A.A. | |||||||||
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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.2 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 22464MC ![]() 7jssC ![]() 7jswC ![]() 7jt1C ![]() 7jt2C ![]() 7jt3C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
+50S ribosomal protein ... , 31 types, 31 molecules bcdefghijklmnopqrstuvwxyzBCDEFa
-30S ribosomal protein ... , 20 types, 20 molecules GHIJKLMNOPQRSTUVWXYZ
#31: Protein | Mass: 25015.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
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#32: Protein | Mass: 23078.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#33: Protein | Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#34: Protein | Mass: 16532.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#35: Protein | Mass: 11669.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#36: Protein | Mass: 16861.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#37: Protein | Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#38: Protein | Mass: 14554.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#39: Protein | Mass: 11196.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#40: Protein | Mass: 12388.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#41: Protein | Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#42: Protein | Mass: 12625.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#43: Protein | Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#44: Protein | Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#45: Protein | Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#46: Protein | Mass: 9263.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#47: Protein | Mass: 7606.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#48: Protein | Mass: 9057.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#49: Protein | Mass: 9506.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#50: Protein | Mass: 7763.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
-RNA chain , 5 types, 5 molecules 31254
#52: RNA chain | Mass: 498724.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
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#53: RNA chain | Mass: 941305.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#54: RNA chain | Mass: 38813.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#55: RNA chain | Mass: 24802.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#56: RNA chain | Mass: 5256.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Protein , 1 types, 1 molecules 8
#57: Protein | Mass: 14709.005 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: arfB, yaeJ, b0191, JW0187 / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: 70S ribosome stalled on truncated mRNA with ArfB bound to the A site. Type: RIBOSOME / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 30.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12528 / Symmetry type: POINT |
NMR ensemble | Conformers submitted total number: 1 |