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Structure paper

TitleStructural basis for RNA-guided DNA degradation by Cas5-HNH/Cascade complex.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 1335, Year 2025
Publish dateFeb 4, 2025
AuthorsYanan Liu / Lin Wang / Qian Zhang / Pengyu Fu / Lingling Zhang / Ying Yu / Heng Zhang / Hongtao Zhu /
PubMed AbstractType I-E CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated proteins) system is one of the most extensively studied RNA-guided adaptive immune systems in ...Type I-E CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated proteins) system is one of the most extensively studied RNA-guided adaptive immune systems in prokaryotes, providing defense against foreign genetic elements. Unlike the previously characterized Cas3 nuclease, which exhibits progressive DNA cleavage in the typical type I-E system, a recently identified HNH-comprising Cascade system enables precise DNA cleavage. Here, we present several near-atomic cryo-electron microscopy (cryo-EM) structures of the Candidatus Cloacimonetes bacterium Cas5-HNH/Cascade complex, both in its DNA-bound and unbound states. Our analysis reveals extensive interactions between the HNH domain and adjacent subunits, including Cas6 and Cas11, with mutations in these key interactions significantly impairing enzymatic activity. Upon DNA binding, the Cas5-HNH/Cascade complex adopts a more compact conformation, with subunits converging toward the center of nuclease, leading to its activation. Notably, we also find that divalent ions such as zinc, cobalt, and nickel down-regulate enzyme activity by destabilizing the Cascade complex. Together, these findings offer structural insights into the assembly and activation of the Cas5-HNH/Cascade complex.
External linksNat Commun / PubMed:39904990 / PubMed Central
MethodsEM (single particle)
Resolution2.47 - 3.1 Å
Structure data

60233

8zlu

EMDB-60233, PDB-8zlu:
Cryo-EM strcuture of Cas5-HNH Cascade,Conf1
Method: EM (single particle) / Resolution: 2.47 Å

60235

8zm3

EMDB-60235, PDB-8zm3:
Cryo-EM strcuture of Cas5-HNH Cascade,apo-Conf2
Method: EM (single particle) / Resolution: 3.1 Å

60297

8zol

EMDB-60297, PDB-8zol:
Cryo-EM strcuture of Cas5-HNH Cascade,Conf3
Method: EM (single particle) / Resolution: 2.55 Å

60328

8zp7

EMDB-60328, PDB-8zp7:
Cryo-EM structure of Cas5-HNH Cascade bound with sDNA, Conf1
Method: EM (single particle) / Resolution: 3.0 Å

60330

8zp9

EMDB-60330, PDB-8zp9:
Cryo-EM structure of Cas5-HNH Cascade bound with sDNA, Conf2
Method: EM (single particle) / Resolution: 2.8 Å

61880

9jxs

EMDB-61880, PDB-9jxs:
Cryo-EM structure of Cas5-HNH Cascade bound with dsDNA
Method: EM (single particle) / Resolution: 2.93 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • candidatus cloacimonetes bacterium adurb.bin088 (bacteria)
  • escherichia coli (E. coli)
KeywordsIMMUNE SYSTEM / Cryo-EM strcuture / Cascade / CRISPR-Cas / IMMUNE SYSTEM/RNA / IMMUNE SYSTEM-RNA complex / IMMUNE SYSTEM/DNA/RNA / IMMUNE SYSTEM-DNA-RNA complex / DNA BINDING PROTEIN

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