5GUH

Crystal structure of silkworm PIWI-clade Argonaute Siwi bound to piRNA

Summary for 5GUH

• Entry DOI: 10.2210/pdb5guh/pdb
• Descriptor: PIWI, RNA (28-MER), MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: nuclease, rnaseh, hydrolase-rna complex, hydrolase/rna
• Biological source: Bombyx mori (Silk moth); More
• Cellular location: Cytoplasm : A8D8P8
• Total number of polymer chains: 2
• Total formula weight: 110558.40

Authors

Matsumoto, N.,Nishimasu, H.,Ishitani, R.,Nureki, O. (deposition date: 2016-08-29, release date: 2016-10-19, Last modification date: 2023-11-08)

Primary citation

Matsumoto, N.,Nishimasu, H.,Sakakibara, K.,Nishida, K.M.,Hirano, T.,Ishitani, R.,Siomi, H.,Siomi, M.C.,Nureki, O.
Crystal Structure of Silkworm PIWI-Clade Argonaute Siwi Bound to piRNA
Cell, 167:484-497.e9, 2016

PubMed Abstract: PIWI-clade Argonaute proteins associate with PIWI-interacting RNAs (piRNAs) and silence transposable elements in animal gonads. Here, we report the crystal structure of a silkworm PIWI-clade Argonaute, Siwi, bound to the endogenous piRNA, at 2.4 Å resolution. Siwi adopts a bilobed architecture consisting of N-PAZ and MID-PIWI lobes, in which the 5' and 3' ends of the bound piRNA are anchored by the MID-PIWI and PAZ domains, respectively. A structural comparison of Siwi with AGO-clade Argonautes reveals notable differences in their nucleic-acid-binding channels, likely reflecting the distinct lengths of their guide RNAs and their mechanistic differences in guide RNA loading and cleavage product release. In addition, the structure reveals that Siwi and prokaryotic, but not eukaryotic, AGO-clade Argonautes share unexpected similarities, such as metal-dependent 5'-phosphate recognition and a potential structural transition during the catalytic-tetrad formation. Overall, this study provides a critical starting point toward a mechanistic understanding of piRNA-mediated transposon silencing.

PubMed: 27693359
DOI: 10.1016/j.cell.2016.09.002

Experimental method

X-RAY DIFFRACTION (2.4 Å)