A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination

    Authors

    Y. Koldobskaya; E. M. Duguid; D. M. Shechner; N. B. Suslov; J. D. Ye; S. S. Sidhu; D. P. Bartel; S. Koide; A. A. Kossiakoff;J. A. Piccirilli

    Comments

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    Abbreviated Journal Title

    Nat. Struct. Mol. Biol.

    Keywords

    X-RAY CRYSTALLOGRAPHY; PROTEIN-PROTEIN INTERACTIONS; I LIGASE RIBOZYME; CRYSTAL-STRUCTURE; BINDING PROTEINS; NONCODING RNA; PHAGE DISPLAY; SELF-CLEAVAGE; CRYSTALLIZATION; COMPLEX; Biochemistry & Molecular Biology; Biophysics; Cell Biology

    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-angstrom 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.

    Journal Title

    Nature Structural & Molecular Biology

    Volume

    18

    Issue/Number

    1

    Publication Date

    1-1-2011

    Document Type

    Article

    Language

    English

    First Page

    100

    Last Page

    +

    WOS Identifier

    WOS:000285966800018

    ISSN

    1545-9985

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