Title

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

Authors

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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