8K9G

Cryo-EM structure of Crt-SPARTA-gRNA-tDNA dimer (conformation-1)

Summary for 8K9G

• Entry DOI: 10.2210/pdb8k9g/pdb
• EMDB information: 36986
• Descriptor: DNA (45-mer), RNA (5'-R(P*UP*GP*AP*GP*GP*UP*AP*GP*UP*AP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*U)-3'), Piwi domain-containing protein, ... (4 entities in total)
• Functional Keywords: ago, dna/rna, dimer, dna binding protein, cell invasion, dna-rna-cell invasion complex, dna/rna/cell invasion
• Biological source: Thermoflavifilum thermophilum; More
• Total number of polymer chains: 8
• Total formula weight: 264190.99

Authors

Gao, X.,Shang, K.,Zhu, K.,Wang, L.,Mu, Z.,Fu, X.,Yu, X.,Qin, B.,Zhu, H.,Ding, W.,Cui, S. (deposition date: 2023-08-01, release date: 2023-10-18, Last modification date: 2024-02-07)

Primary citation

Gao, X.,Shang, K.,Zhu, K.,Wang, L.,Mu, Z.,Fu, X.,Yu, X.,Qin, B.,Zhu, H.,Ding, W.,Cui, S.
Nucleic-acid-triggered NADase activation of a short prokaryotic Argonaute.
Nature, 625:822-831, 2024

PubMed Abstract: Argonaute (Ago) proteins mediate RNA- or DNA-guided inhibition of nucleic acids. Although the mechanisms used by eukaryotic Ago proteins and long prokaryotic Ago proteins (pAgos) are known, that used by short pAgos remains elusive. Here we determined the cryo-electron microscopy structures of a short pAgo and the associated TIR-APAZ proteins (SPARTA) from Crenotalea thermophila (Crt): a free-state Crt-SPARTA; a guide RNA-target DNA-loaded Crt-SPARTA; two Crt-SPARTA dimers with distinct TIR organization; and a Crt-SPARTA tetramer. These structures reveal that Crt-SPARTA is composed of a bilobal-fold Ago lobe that connects with a TIR lobe. Whereas the Crt-Ago contains a MID and a PIWI domain, Crt-TIR-APAZ has a TIR domain, an N-like domain, a linker domain and a trigger domain. The bound RNA-DNA duplex adopts a B-form conformation that is recognized by base-specific contacts. Nucleic acid binding causes conformational changes because the trigger domain acts as a 'roadblock' that prevents the guide RNA 5' ends and the target DNA 3' ends from reaching their canonical pockets; this disorders the MID domain and promotes Crt-SPARTA dimerization. Two RNA-DNA-loaded Crt-SPARTA dimers form a tetramer through their TIR domains. Four Crt-TIR domains assemble into two parallel head-to-tail-organized TIR dimers, indicating an NADase-active conformation, which is supported by our mutagenesis study. Our results reveal the structural basis of short-pAgo-mediated defence against invading nucleic acids, and provide insights for optimizing the detection of SPARTA-based programmable DNA sequences.

PubMed: 37783228
DOI: 10.1038/s41586-023-06665-6

Experimental method

ELECTRON MICROSCOPY (3.49 Å)