Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	ArfB can displace mRNA to rescue stalled ribosomes.
Journal, issue, pages	Nat Commun, Vol. 11, Issue 1, Page 5552, Year 2020
Publish date	Nov 3, 2020
Authors	Christine E Carbone / Gabriel Demo / Rohini Madireddy / Egor Svidritskiy / Andrei A Korostelev /
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 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.
External links	Nat Commun / PubMed:33144582 / PubMed Central
Methods	EM (single particle)
Resolution	3.2 - 3.8 Å
Structure data	22459 7jss EMDB-22459, PDB-7jss: ArfB Rescue of a 70S Ribosome stalled on truncated mRNA with a partial A-site codon (+2-II) Method: EM (single particle) / Resolution: 3.7 Å 22461 7jsw EMDB-22461, PDB-7jsw: ArfB Rescue of a 70S Ribosome stalled on truncated mRNA with a partial A-site codon (+2-III) Method: EM (single particle) / Resolution: 3.8 Å 22464 7jsz EMDB-22464, PDB-7jsz: ArfB Rescue of a 70S Ribosome stalled on truncated mRNA with a partial A-site codon (+2-IV) Method: EM (single particle) / Resolution: 3.7 Å EMDB-22465: 70S ribosome stalled on truncated mRNA Method: EM (single particle) / Resolution: 3.7 Å 22466 7jt1 EMDB-22466, PDB-7jt1: 70S ribosome stalled on long mRNA with ArfB-1 and ArfB-2 bound (+9-III) Method: EM (single particle) / Resolution: 3.3 Å EMDB-22467: 70S rotated ribosome stalled on truncated mRNA Method: EM (single particle) / Resolution: 3.4 Å EMDB-22468: 70S ribosome stalled on long mRNA with ArfB C-terminus bound in the mRNA tunnel Method: EM (single particle) / Resolution: 3.4 Å 22469 7jt2 EMDB-22469, PDB-7jt2: 70S ribosome stalled on long mRNA with ArfB bound in the A site Method: EM (single particle) / Resolution: 3.5 Å EMDB-22470: 70S ribosome stalled on long mRNA with ArfB bound in the A site (+9-VI) Method: EM (single particle) / Resolution: 3.2 Å EMDB-22471: Rotated 70S ribosome stalled on long mRNA with ArfB-1 bound in the A site (+9-V) Method: EM (single particle) / Resolution: 3.3 Å 22472 7jt3 EMDB-22472, PDB-7jt3: Rotated 70S ribosome stalled on long mRNA with ArfB-1 and ArfB-2 bound in the A site (+9-IV) Method: EM (single particle) / Resolution: 3.7 Å
Source	escherichia coli (strain k12) (bacteria) escherichia coli k-12 (bacteria) escherichia coli (E. coli)
Keywords	Ribosome/TRANSLATION / Ribosome / ArfB / mRNA / TRANSLATION / Ribosome-TRANSLATION complex