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TitleStructure of the OMEGA nickase IsrB in complex with ωRNA and target DNA.
Journal, issue, pagesNature, Vol. 610, Issue 7932, Page 575-581, Year 2022
Publish dateOct 12, 2022
AuthorsSeiichi Hirano / Kalli Kappel / Han Altae-Tran / Guilhem Faure / Max E Wilkinson / Soumya Kannan / F Esra Demircioglu / Rui Yan / Momoko Shiozaki / Zhiheng Yu / Kira S Makarova / Eugene V Koonin / Rhiannon K Macrae / Feng Zhang /
PubMed AbstractRNA-guided systems, such as CRISPR-Cas, combine programmable substrate recognition with enzymatic function, a combination that has been used advantageously to develop powerful molecular technologies. ...RNA-guided systems, such as CRISPR-Cas, combine programmable substrate recognition with enzymatic function, a combination that has been used advantageously to develop powerful molecular technologies. Structural studies of these systems have illuminated how the RNA and protein jointly recognize and cleave their substrates, guiding rational engineering for further technology development. Recent work identified a new class of RNA-guided systems, termed OMEGA, which include IscB, the likely ancestor of Cas9, and the nickase IsrB, a homologue of IscB lacking the HNH nuclease domain. IsrB consists of only around 350 amino acids, but its small size is counterbalanced by a relatively large RNA guide (roughly 300-nt ωRNA). Here, we report the cryogenic-electron microscopy structure of Desulfovirgula thermocuniculi IsrB (DtIsrB) in complex with its cognate ωRNA and a target DNA. We find the overall structure of the IsrB protein shares a common scaffold with Cas9. In contrast to Cas9, however, which uses a recognition (REC) lobe to facilitate target selection, IsrB relies on its ωRNA, part of which forms an intricate ternary structure positioned analogously to REC. Structural analyses of IsrB and its ωRNA as well as comparisons to other RNA-guided systems highlight the functional interplay between protein and RNA, advancing our understanding of the biology and evolution of these diverse systems.
External linksNature / PubMed:36224386 / PubMed Central
MethodsEM (single particle)
Resolution3.1 - 6.9 Å
Structure data

EMDB-26723: Structure of IsrB ternary complex with RNA mutant and target DNA
Method: EM (single particle) / Resolution: 6.9 Å

27533

8dmb

EMDB-27533, PDB-8dmb:
Structure of Desulfovirgula thermocuniculi IsrB (DtIsrB) in complex with omega RNA and target DNA
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • desulfovirgula thermocuniculi (bacteria)
  • synthetic construct (others)
  • saccharomyces cerevisiae s288c (yeast)
KeywordsRNA BINDING PROTEIN/RNA/DNA / Endonuclease / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA-DNA complex / Transposon / CRISPR / IS200/IS605

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