Crystal structure of a zinc-finger–RNA complex reveals two modes of molecular recognition

Duo Lu, M. Alexandra Searles and Aaron Klug ()
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Duo Lu: Medical Research Council (MRC) Laboratory of Molecular Biology
M. Alexandra Searles: Medical Research Council (MRC) Laboratory of Molecular Biology
Aaron Klug: Medical Research Council (MRC) Laboratory of Molecular Biology

Nature, 2003, vol. 426, issue 6962, 96-100

Abstract: Abstract Zinc-finger proteins of the classical Cys2His2 type are the most frequently used class of transcription factor and account for about 3% of genes in the human genome1,2. The zinc-finger motif was discovered3 during biochemical studies on the transcription factor TFIIIA, which regulates the 5S ribosomal RNA genes of Xenopus laevis4,5. Zinc-fingers mostly interact with DNA, but TFIIIA binds not only specifically to the promoter DNA, but also to 5S RNA itself6,7,8,9. Increasing evidence indicates that zinc-fingers are more widely used to recognize RNA10,11,12,13. There have been numerous structural studies on DNA binding14, but none on RNA binding by zinc-finger proteins. Here we report the crystal structure of a three-finger complex with 61 bases of RNA, derived15 from the central regions of the complete nine-finger TFIIIA–5S RNA complex. The structure reveals two modes of zinc-finger binding, both of which differ from that in common use for DNA: first, the zinc-fingers interact with the backbone of a double helix; and second, the zinc-fingers specifically recognize individual bases positioned for access in otherwise intricately folded ‘loop’ regions of the RNA.

Date: 2003
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DOI: 10.1038/nature02088

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