A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity
- National Institute of Environmental Health Sciences, National Institutes of Health, United States
- University of Texas at Dallas, United States
Abstract
In the Caenorhabditis elegans germline, fem-3 Binding Factor (FBF) partners with LST-1 to maintain stem cells. A crystal structure of an FBF-2/LST-1/RNA complex revealed that FBF-2 recognizes a short RNA motif different from the characteristic 9-nt FBF binding element, and compact motif recognition coincided with curvature changes in the FBF-2 scaffold. Previously we engineered FBF-2 to favor recognition of shorter RNA motifs without curvature change (Bhat, Qiu, et al. 2019). In vitro selection of RNAs bound by FBF-2 suggested sequence specificity in the central region of the compact element. This bias, reflected in the crystal structure, was validated in RNA-binding assays. FBF-2 has the intrinsic ability to bind to this shorter motif. LST-1 weakens FBF-2 binding affinity for short and long motifs, which may increase target selectivity. Our findings highlight the role of FBF scaffold flexibility in RNA recognition and suggest a new mechanism by which protein partners refine target site selection.
Data availability
Atomic coordinates and structure factors are deposited under RCSB PDB ID 6PUN. SEQRS sequence data are available through the Dryad Digital Repository, accession number doi:10.5061/dryad.30501q7.
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SEQRS data for FBF-2 and SEQRS data for the LST-1 FBF-2 complexDryad Digital Repository, doi:10.5061/dryad.30501q7.
Article and author information
Author details
Zachary T Campbell
Traci M T Tanaka Hall
Funding
National Institutes of Health (ZIA ES50165)
- Traci M T Tanaka Hall
National Institutes of Health (R01NS100788)
- Zachary T Campbell
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Timothy W Nilsen, Case Western Reserve University, United States
Version history
- Received: June 4, 2019
- Accepted: August 9, 2019
- Accepted Manuscript published: August 9, 2019 (version 1)
- Version of Record published: August 16, 2019 (version 2)
- Version of Record updated: August 30, 2019 (version 3)
Copyright
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
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A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity
eLife 8:e48968.
https://doi.org/10.7554/eLife.48968
Further reading
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