8PVV

Archaeoglobus fulgidus AfAgo complex with AfAgo-N protein (fAfAgo) bound with 30 nt RNA guide and 51 nt DNA target

Summary for 8PVV

• Entry DOI: 10.2210/pdb8pvv/pdb
• Related: 8ok9
• EMDB information: 17973
• Descriptor: Piwi protein, Archaeoglobus fulgidus AfAgo-N protein, RNA (30-MER), ... (6 entities in total)
• Functional Keywords: argonaute, piwi domain, protein-dna complex, dna binding protein
• Biological source: Archaeoglobus fulgidus; More
• Total number of polymer chains: 4
• Total formula weight: 106056.19

Authors

Manakova, E.N.,Zaremba, M.,Pocevicuite, R.,Golovinas, E.,Sasnauskas, G.,Zagorskaite, E.,Silanskas, A. (deposition date: 2023-07-18, release date: 2024-01-24, Last modification date: 2024-03-27)

Primary citation

Manakova, E.,Golovinas, E.,Poceviciute, R.,Sasnauskas, G.,Silanskas, A.,Rutkauskas, D.,Jankunec, M.,Zagorskaite, E.,Jurgelaitis, E.,Grybauskas, A.,Venclovas, C.,Zaremba, M.
The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein.
Nucleic Acids Res., 52:2530-2545, 2024

PubMed Abstract: Argonaute (Ago) proteins are present in all three domains of life (bacteria, archaea and eukaryotes). They use small (15-30 nucleotides) oligonucleotide guides to bind complementary nucleic acid targets and are responsible for gene expression regulation, mobile genome element silencing, and defence against viruses or plasmids. According to their domain organization, Agos are divided into long and short Agos. Long Agos found in prokaryotes (long-A and long-B pAgos) and eukaryotes (eAgos) comprise four major functional domains (N, PAZ, MID and PIWI) and two structural linker domains L1 and L2. The majority (∼60%) of pAgos are short pAgos, containing only the MID and inactive PIWI domains. Here we focus on the prokaryotic Argonaute AfAgo from Archaeoglobus fulgidus DSM4304. Although phylogenetically classified as a long-B pAgo, AfAgo contains only MID and catalytically inactive PIWI domains, akin to short pAgos. We show that AfAgo forms a heterodimeric complex with a protein encoded upstream in the same operon, which is a structural equivalent of the N-L1-L2 domains of long pAgos. This complex, structurally equivalent to a long PAZ-less pAgo, outperforms standalone AfAgo in guide RNA-mediated target DNA binding. Our findings provide a missing piece to one of the first and the most studied pAgos.

PubMed: 38197228
DOI: 10.1093/nar/gkad1241

Experimental method

ELECTRON MICROSCOPY (2.81 Å)