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Analysis of RNA Processing Reactions Using Cell Free Systems: 3' End Cleavage of Pre-mRNA Substrates in vitro

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Structural basis for single-stranded RNA recognition and cleavage by C3PO.

Jing Zhang¹, Hehua Liu^1,2, Qingqing Yao²

¹Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China.

Nucleic Acids Research

|September 7, 2016

Summary

Translin-associated factor-x (C3PO) complexes are crucial for RNA interference. We determined the structures of Nanoarchaeum equitans C3PO, revealing substrate binding and catalytic mechanisms essential for RNAi pathway function.

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Last Updated: Mar 15, 2026

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DNAzyme-dependent Analysis of rRNA 2’-O-Methylation

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Published on: September 16, 2019

Area of Science:

Biochemistry
Molecular Biology
Structural Biology

Background:

Translin and translin-associated factor-x form conserved C3PO complexes in eukaryotes.
These complexes are involved in nucleic acid metabolism and RNA interference (RNAi).
In humans and Drosophila, C3POs process siRNA passenger strands, activating the RNA-induced silencing complex.

Purpose of the Study:

To elucidate the structural basis of C3PO function in Nanoarchaeum equitans.
To understand substrate binding and catalytic mechanisms in C3POs.

Main Methods:

X-ray crystallography to determine the structures of apo-NeC3PO, NeC3PO:ssRNA, and NeC3PO:ssDNA complexes.
Site-directed mutagenesis.
In vitro cleavage assays.

Main Results:

The apo-NeC3PO structure revealed an open conformation with a potential substrate entryway.
NeC3PO:ssRNA and NeC3PO:ssDNA complexes adopted a closed, football-like structure, capturing substrates internally.
The catalytic NeC3PO:ssRNA structure provided insights into substrate binding and a conserved two-cation-assisted catalytic mechanism.

Conclusions:

The determined structures offer the first view of a catalytic C3PO complex.
This work advances the understanding of RNAi pathway mechanisms and conserved C3PO functions across eukaryotes.