Nucleic Acids Research, 2000, Vol. 28, No. 23 4611-4616
© 2000 Oxford University Press
Deletion of a single hydrogen bonding atom from the MS2 RNA operator leads to dramatic rearrangements at the RNA–coat protein interface
Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden, 1Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK, 2Ribozyme Pharmaceutical Inc., 2950 Wilderness Place, Boulder, CO 80301, USA and 3School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
The MS2 coat protein binds specifically to an RNA hairpin formed within the viral genome. By soaking different RNA fragments into crystals of MS2 coat protein capsids it is possible to determine the X-ray structure of the RNA–protein complexes formed. Here we present the structure to 2.85 Å resolution of a complex between a chemically modified RNA hairpin variant and the MS2 coat protein. This RNA variant has a substitution at the –5 base position, which has been shown previously to be pyrimidine-specific and is a uracil in the wild-type RNA. The modified RNA hairpin contains a pyridin-4-one base (4one) at this position that lacks the exocyclic 2-oxygen eliminating the possibility of forming a hydrogen bond to asparagine A87 in the protein. The 4one complex structure shows an unprecedented major conformational change in the loop region of the RNA, whereas there is almost no change in the conformation of the protein.
* To whom correspondence should be addressed. Tel: +46 18 471 48 45; Fax: +46 18 53 69 71; Email: lars{at}xray.bmc.uu.se
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