5mdy

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Structure of ArfA and TtRF2 bound to the 70S ribosome (pre-accommodated state)

Structural highlights

5mdy is a 10 chain structure with sequence from Escherichia coli, Escherichia coli K-12 and Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Electron Microscopy, Resolution 3.35Å
Experimental data:Check to display Experimental Data
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RS19_ECOLI In the E.coli 70S ribosome in the initiation state (PubMed:12809609) it has been modeled to contact the 23S rRNA of the 50S subunit forming part of bridge B1a; this bridge is broken in the model with bound EF-G. The 23S rRNA contact site in bridge B1a is modeled to differ in different ribosomal states (PubMed:12859903), contacting alternately S13 or S19. In the 3.5 angstroms resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 bridge B1b are different, confirming the dynamic nature of this interaction. Bridge B1a is not visible in the crystallized ribosomes due to 23S rRNA disorder.[HAMAP-Rule:MF_00531] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Contacts the A site tRNA.[HAMAP-Rule:MF_00531]

Publication Abstract from PubMed

Ribosomes stall when they encounter the end of messenger RNA (mRNA) without an in-frame stop codon. In bacteria, these "nonstop" complexes can be rescued by alternative ribosome-rescue factor A (ArfA). We used electron cryomicroscopy to determine structures of ArfA bound to the ribosome with 3'-truncated mRNA, at resolutions ranging from 3.0 to 3.4 angstroms. ArfA binds within the ribosomal mRNA channel and substitutes for the absent stop codon in the A site by specifically recruiting release factor 2 (RF2), initially in a compact preaccommodated state. A similar conformation of RF2 may occur on stop codons, suggesting a general mechanism for release-factor-mediated translational termination in which a conformational switch leads to peptide release only when the appropriate signal is present in the A site.

Translational termination without a stop codon.,James NR, Brown A, Gordiyenko Y, Ramakrishnan V Science. 2016 Dec 16;354(6318):1437-1440. Epub 2016 Dec 1. PMID:27934701[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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Citations
9 reviews cite this structure
Quality controls induced by aberrant translation.
Inada et al. (2020)
8 more
34 other articles
No citations found

See Also

References

  1. ↑ James NR, Brown A, Gordiyenko Y, Ramakrishnan V. Translational termination without a stop codon. Science. 2016 Dec 16;354(6318):1437-1440. Epub 2016 Dec 1. PMID:27934701 doi:http://dx.doi.org/10.1126/science.aai9127

Contents


5mdy, resolution 3.35Å

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