8PVV image
Entry Detail
PDB ID:
8PVV
EMDB ID:
Title:
Archaeoglobus fulgidus AfAgo complex with AfAgo-N protein (fAfAgo) bound with 30 nt RNA guide and 51 nt DNA target
Biological Source:
PDB Version:
Deposition Date:
2023-07-18
Release Date:
2024-01-24
Method Details:
Experimental Method:
Resolution:
2.81 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Piwi protein
Chain IDs:A
Chain Length:427
Number of Molecules:1
Biological Source:Archaeoglobus fulgidus
Polymer Type:polypeptide(L)
Description:Archaeoglobus fulgidus AfAgo-N protein
Mutations:N-terminal His tag
Chain IDs:B (auth: C)
Chain Length:273
Number of Molecules:1
Biological Source:Archaeoglobus fulgidus DSM 8774
Polymer Type:polyribonucleotide
Description:RNA (30-MER)
Chain IDs:C (auth: R)
Chain Length:30
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polydeoxyribonucleotide
Description:DNA (51-MER)
Chain IDs:D (auth: S)
Chain Length:51
Number of Molecules:1
Biological Source:Escherichia coli
Ligand Molecules
Primary Citation
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)
PMID: 38197228 DOI: 10.1093/nar/gkad1241

Abstact

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.

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Primary Citation of related structures