7JSW | pdb_00007jsw

ArfB Rescue of a 70S Ribosome stalled on truncated mRNA with a partial A-site codon (+2-III)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

ArfB can displace mRNA to rescue stalled ribosomes.

Carbone, C.E., Demo, G., Madireddy, R., Svidritskiy, E., Korostelev, A.A.

(2020) Nat Commun 11: 5552-5552

  • DOI: https://doi.org/10.1038/s41467-020-19370-z
  • Primary Citation of Related Structures:  
    7JSS, 7JSW, 7JSZ, 7JT1, 7JT2, 7JT3

  • PubMed 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 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.

    • Organizational Affiliation: 
    • RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2A [auth b]271Escherichia coli K-12Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3B [auth c]209Escherichia coli K-12Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4C [auth d]201Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5D [auth e]177Escherichia coli K-12Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6E [auth f]176Escherichia coli K-12Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9F [auth g]149Escherichia coli K-12Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13G [auth j]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14H [auth k]122Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15I [auth l]143Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16J [auth m]136Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17K [auth n]120Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18L [auth o]116Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19M [auth p]114Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20N [auth q]117Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21O [auth r]103Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22P [auth s]110Escherichia coli K-12Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23Q [auth t]93Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24R [auth u]102Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25S [auth v]94Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27T [auth w]75Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28U [auth x]77Escherichia coli K-12Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29V [auth y]63Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30W [auth z]58Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32X [auth B]56Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33Y [auth C]50Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34Z [auth D]46Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35AA [auth E]64Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36BA [auth F]38Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2CA [auth G]225Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3DA [auth H]206Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4EA [auth I]205Escherichia coli K-12Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5FA [auth J]157Escherichia coli K-12Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6GA [auth K]100Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S7HA [auth L]151Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8IA [auth M]129Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9JA [auth N]127Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10KA [auth O]98Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11LA [auth P]116Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12MA [auth Q]123Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13NA [auth R]114Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14OA [auth S]100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15PA [auth T]88Escherichia coli K-12Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16QA [auth U]82Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17RA [auth V]80Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18SA [auth W]65Escherichia coli K-12Mutation(s): 0 
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UniProt GroupP0A7T7
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19TA [auth X]79Escherichia coli K-12Mutation(s): 0 
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UniProt GroupP0A7U3
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20UA [auth Y]85Escherichia coli K-12Mutation(s): 0 
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UniProt GroupP0A7U7
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21VA [auth Z]65Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase ArfBBB [auth 8]132Escherichia coli K-12Mutation(s): 0 
Gene Names: arfB, yaeJ, b0191, JW0187
EC: 3.1.1.29
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Find proteins for P40711 (Escherichia coli (strain K12))
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UniProt GroupP40711
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Entity ID: 49
MoleculeChains LengthOrganismImage
16S ribosomal RNAWA [auth 3]1,539Escherichia coli K-12
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Entity ID: 50
MoleculeChains LengthOrganismImage
23S ribosomal RNAXA [auth 1]2,903Escherichia coli K-12
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Entity ID: 51
MoleculeChains LengthOrganismImage
5S ribosomal RNAYA [auth 2]120Escherichia coli K-12
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Entity ID: 52
MoleculeChains LengthOrganismImage
tRNAfMetZA [auth 5]77Escherichia coli K-12
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Entity ID: 53
MoleculeChains LengthOrganismImage
mRNAAB [auth 4]16Escherichia coli K-12
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM107465
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM127094

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2020-11-18
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references