A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination
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Author(s)
Koldobskaya, Yelena
Duguid, Erica M.
Shechner, David M.
Suslov, Nikolai B.
Ye, Jingdong
Sidhu, Sachdev S.
Bartel, David
Koide, Shohei
Kossiakoff, Anthony A.
Piccirilli, Joseph A.
Date Issued
December 2010
Journal
Nature Structural and Molecular Biology
Publisher
Nature Publishing Group
Citation
Koldobskaya, Yelena et al. “A Portable RNA Sequence Whose Recognition by a Synthetic Antibody Facilitates Structural Determination.” Nature Structural & Molecular Biology 18.1 (2010): 100–106.
Version
Author's final manuscript
Abstract
RNA crystallization and phasing represent major bottlenecks in RNA structure determination. Seeking to exploit antibody fragments as RNA crystallization chaperones, we have used an arginine-enriched synthetic Fab library displayed on phage to obtain Fabs against the class I ligase ribozyme. We solved the structure of a Fab–ligase complex at 3.1-Å resolution using molecular replacement with Fab coordinates, confirming the ribozyme architecture and revealing the chaperone's role in RNA recognition and crystal contacts. The epitope resides in the GAAACAC sequence that caps the P5 helix, and this sequence retains high-affinity Fab binding within the context of other structured RNAs. This portable epitope provides a new RNA crystallization chaperone system that easily can be screened in parallel to the U1A RNA-binding protein, with the advantages of a smaller loop and Fabs′ high molecular weight, large surface area and phasing power.
MIT Department
Massachusetts Institute of Technology. Department of Biology
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Creative Commons Attribution-Noncommercial-Share Alike 3.0
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DOI of Published Version
https://doi.org/10.1038/nsmb.1945
