8IFK

Cryo-EM structure of monomeric SPARTA gRNA-ssDNA target complex

Summary for 8IFK

• Entry DOI: 10.2210/pdb8ifk/pdb
• EMDB information: 35419
• Descriptor: TIR domain-containing protein, Piwi domain-containing protein, guide RNA, ... (5 entities in total)
• Functional Keywords: rna binding protein-rna-dna complex, rna binding protein/rna/dna
• Biological source: Thermoflavifilum thermophilum; More
• Total number of polymer chains: 4
• Total formula weight: 125925.87

Authors

Zhang, J.T.,Jia, N. (deposition date: 2023-02-18, release date: 2024-01-17, Last modification date: 2024-04-10)

Primary citation

Zhang, J.T.,Wei, X.Y.,Cui, N.,Tian, R.,Jia, N.
Target ssDNA activates the NADase activity of prokaryotic SPARTA immune system.
Nat.Chem.Biol., 20:503-511, 2024

PubMed Abstract: Argonaute proteins (Agos), which use small RNAs or DNAs as guides to recognize complementary nucleic acid targets, mediate RNA silencing in eukaryotes. In prokaryotes, Agos are involved in immunity: the short prokaryotic Ago/TIR-APAZ (SPARTA) immune system triggers cell death by degrading NAD in response to invading plasmids, but its molecular mechanisms remain unknown. Here we used cryo-electron microscopy to determine the structures of inactive monomeric and active tetrameric Crenotalea thermophila SPARTA complexes, revealing mechanisms underlying SPARTA assembly, RNA-guided recognition of target single-stranded DNA (ssDNA) and subsequent SPARTA tetramerization, as well as tetramerization-dependent NADase activation. The small RNA guides Ago to recognize its ssDNA target, inducing SPARTA tetramerization via both Ago- and TIR-mediated interactions and resulting in a two-stranded, parallel, head-to-tail TIR rearrangement primed for NAD hydrolysis. Our findings thus identify the molecular basis for target ssDNA-mediated SPARTA activation, which will facilitate the development of SPARTA-based biotechnological tools.

PubMed: 37932528
DOI: 10.1038/s41589-023-01479-z

Experimental method

ELECTRON MICROSCOPY (2.54 Å)