1YTU

Structural basis for 5'-end-specific recognition of the guide RNA strand by the A. fulgidus PIWI protein

Summary for 1YTU

• Entry DOI: 10.2210/pdb1ytu/pdb
• Descriptor: 5'-R(P*AP*GP*AP*CP*AP*G)-3', 5'-R(P*UP*GP*UP*C)-3', hypothetical protein AF1318, ... (5 entities in total)
• Functional Keywords: protein-rna complex, rna duplex, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Archaeoglobus fulgidus
• Total number of polymer chains: 6
• Total formula weight: 105997.19

Authors

Ma, J.B.,Yuan, Y.R.,Meister, G.,Pei, Y.,Tuschl, T.,Patel, D.J. (deposition date: 2005-02-11, release date: 2005-04-05, Last modification date: 2024-10-16)

Primary citation

Ma, J.B.,Yuan, Y.R.,Meister, G.,Pei, Y.,Tuschl, T.,Patel, D.J.
Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus Piwi protein.
Nature, 434:666-670, 2005

PubMed Abstract: RNA interference (RNAi) is a conserved sequence-specific gene regulatory mechanism mediated by the RNA-induced silencing complex (RISC), which is composed of a single-stranded guide RNA and an Argonaute protein. The PIWI domain, a highly conserved motif within Argonaute, has been shown to adopt an RNase H fold critical for the endonuclease cleavage activity of RISC. Here we report the crystal structure of Archaeoglobus fulgidus Piwi protein bound to double-stranded RNA, thereby identifying the binding pocket for guide-strand 5'-end recognition and providing insight into guide-strand-mediated messenger RNA target recognition. The phosphorylated 5' end of the guide RNA is anchored within a highly conserved basic pocket, supplemented by the carboxy-terminal carboxylate and a bound divalent cation. The first nucleotide from the 5' end of the guide RNA is unpaired and stacks over a conserved tyrosine residue, whereas successive nucleotides form a four-base-pair RNA duplex. Mutation of the corresponding amino acids that contact the 5' phosphate in human Ago2 resulted in attenuated mRNA cleavage activity. Our structure of the Piwi-RNA complex, and that determined elsewhere, provide direct support for the 5' region of the guide RNA serving as a nucleation site for pairing with target mRNA and for a fixed distance separating the RISC-mediated mRNA cleavage site from the anchored 5' end of the guide RNA.

PubMed: 15800629
DOI: 10.1038/nature03514

Experimental method

X-RAY DIFFRACTION (2.5 Å)