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TitleAssessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit.
Journal, issue, pagesNucleic Acids Res, Vol. 48, Issue 5, Page 2723-2732, Year 2020
Publish dateMar 18, 2020
AuthorsVanja Stojković / Alexander G Myasnikov / Iris D Young / Adam Frost / James S Fraser / Danica Galonić Fujimori /
PubMed AbstractPost-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been ...Post-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA structure and regulation of ribosome biogenesis and protein synthesis. In some instances, rRNA modifications can confer antibiotic resistance. High-resolution ribosome structures are thus necessary for precise determination of modified nucleotides' positions, a task that has previously been accomplished by X-ray crystallography. Here, we present a cryo-electron microscopy (cryo-EM) structure of the Escherichia coli 50S subunit at an average resolution of 2.2 Å as an additional approach for mapping modification sites. Our structure confirms known modifications present in 23S rRNA and additionally allows for localization of Mg2+ ions and their coordinated water molecules. Using our cryo-EM structure as a testbed, we developed a program for assessment of cryo-EM map quality. This program can be easily used on any RNA-containing cryo-EM structure, and an associated Coot plugin allows for visualization of validated modifications, making it highly accessible.
External linksNucleic Acids Res / PubMed:31989172 / PubMed Central
MethodsEM (single particle)
Resolution2.2 Å
Structure data

20353

6pj6

EMDB-20353, PDB-6pj6:
High resolution cryo-EM structure of E.coli 50S
Method: EM (single particle) / Resolution: 2.2 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-NA:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER

Source
  • escherichia coli (E. coli)
  • Escherichia coli
KeywordsRIBOSOME

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