8K34

Cryo-EM structure of SPARTA gRNA binary complex

Summary for 8K34

• Entry DOI: 10.2210/pdb8k34/pdb
• EMDB information: 36843
• Descriptor: TIR domain-containing protein, Piwi domain-containing protein, RNA (5'-R(P*AP*AP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*AP*GP*U)-3'), ... (4 entities in total)
• Functional Keywords: structural protein-rna complex, structural protein/rna
• Biological source: Thermoflavifilum thermophilum; More
• Total number of polymer chains: 3
• Total formula weight: 118244.88

Authors

Zhang, J.T.,Jia, N. (deposition date: 2023-07-14, 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 (2.81 Å)