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TitleCryo-EM structure of Archaeoglobus fulgidus type III-B CRISPR-Cas effector and intermediate crRNA processing during effector assembly.
Journal, issue, pagesBiochem Biophys Res Commun, Vol. 792, Page 152978, Year 2025
Publish dateDec 15, 2025
AuthorsKazuki Ishihara / Sumire Kitagawa / Naruhiko Adachi / Masato Akutsu / Toshiya Senda / Hideko Inanaga / Tomoyuki Numata /
PubMed AbstractType III CRISPR-Cas effectors recognize target RNAs complementary to the crRNA guide, activating diverse downstream antiviral responses. In contrast to type III-A systems, the architecture of the ...Type III CRISPR-Cas effectors recognize target RNAs complementary to the crRNA guide, activating diverse downstream antiviral responses. In contrast to type III-A systems, the architecture of the type III-B effector (Cmr), comprising six proteins (Cmr1-Cmr6) and a crRNA, remains incompletely defined. Moreover, although maturation of the 3' region of type III crRNA has been attributed to polynucleotide phosphorylase (PNPase), an alternative maturation pathway has been suggested but remains to be elucidated. Here we determined the cryo-EM structure of the Cmr1-lacking Archaeoglobus fulgidus Cmr (AfCmrΔ1) bound to a target analog at 3.4 Å resolution. The complex forms a continuous basic channel that accommodates a crRNA-target heteroduplex. Comparative interface analysis explains why the previously reported cross-species Cmr assembly retains activity, revealing interface flexibility that enables compatible Cmr3-Cmr4 and Cmr2-Cmr5 interactions. Furthermore, we show the cooperative, site-specific processing of an intermediate crRNA that requires both AfCmrΔ1 and AfCmr1 and proceeds without divalent cations. In addition to identifying the cleavage site within the intermediate crRNA, mutational analysis of AfCmr1 reveals residues critical for the reaction. These findings suggest an alternative pathway for crRNA maturation during type III effector assembly that complements PNPase-mediated trimming of the intermediate crRNA, thereby expanding the mechanistic landscape of type III CRISPR-Cas systems.
External linksBiochem Biophys Res Commun / PubMed:41242302
MethodsEM (single particle)
Resolution3.4 Å
Structure data

66472

9x25

EMDB-66472, PDB-9x25:
Target analog-bound type III-B Cmr complex of Archaeoglobus fulgidus
Method: EM (single particle) / Resolution: 3.4 Å

Source
  • archaeoglobus fulgidus dsm 4304 (archaea)
  • pyrococcus furiosus dsm 3638 (archaea)
  • synthetic construct (others)
KeywordsRNA BINDING PROTEIN/RNA/DNA / Type III-B CRISPR-Cas effector / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA-DNA complex

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