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The molecular architecture of human Dicer

Abstract

Dicer is a multidomain enzyme that generates small RNAs for gene silencing in eukaryotes. Current understanding of Dicer structure is restricted to simple forms of the enzyme, whereas that of the large and complex Dicer in metazoans is unknown. Here we describe a new domain localization strategy developed to determine the structure of human Dicer by EM. A rearrangement of the nuclease core, compared to the archetypal Giardia lamblia Dicer, explains how metazoan Dicers generate products that are 21–23 nucleotides in length. The helicase domains form a clamp-like structure adjacent to the RNase III active site, facilitating recognition of pre-miRNA loops or translocation on long dsRNAs. Drosophila melanogaster Dicer-2 shows similar features, revealing that the three-dimensional architecture is conserved. These results illuminate the structural basis for small RNA production in eukaryotes and provide a versatile new tool for determining structures of large molecular machines.

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Figure 1: The conserved domain structure of metazoan Dicer.
Figure 2: Mapping the nuclease core of human Dicer.
Figure 3: Comparison of the human Dicer and G. lamblia Dicer nuclease cores.
Figure 4: The helicase forms a clamp-like structure in the base.
Figure 5: Conformational states of the Dicer helicase.
Figure 6: Comparison of human and D. melanogaster Dicer structures.
Figure 7: Architecture and mechanism of Dicer.

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Acknowledgements

We are grateful to D.K. Simanshu, Y. Tian and D.J. Patel (Memorial Sloan-Kettering Cancer Center) for sharing the human Dicer PAZ-platform structure before publication. EM imaging and reconstruction was conducted at the National Resource for Automated Molecular Microscopy, which is supported by the US National Institutes of Health (NIH) through the P41 program of the National Center for Research Resources (RR017573) and the National Institute of General Medical Sciences (GM103310). This work was also supported by NIH grant R01 GM086701 to I.J.M. P.-W.L. is a predoctoral fellow of the American Heart Association. I.J.M. is a Pew Scholar in the Biomedical Sciences.

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C.S.P., B.C. and I.J.M. conceived of the project. P.-W.L., K.Z.G. and N.D. prepared the samples. P.-W.L. carried out the data collection. P.-W.L., C.S.P., B.C. and I.J.M. analyzed the data. P.-W.L. and I.J.M. wrote the manuscript.

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Correspondence to Bridget Carragher or Ian J MacRae.

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Lau, PW., Guiley, K., De, N. et al. The molecular architecture of human Dicer. Nat Struct Mol Biol 19, 436–440 (2012). https://doi.org/10.1038/nsmb.2268

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