6PUN

Crystal structure of a ternary complex of FBF-2 with LST-1 (site B) and compact FBE RNA

Summary for 6PUN

• Entry DOI: 10.2210/pdb6pun/pdb
• Descriptor: Fem-3 mRNA-binding factor 2, RNA (5'-R(*CP*UP*GP*UP*GP*AP*AP*U)-3'), LST-1, ... (7 entities in total)
• Functional Keywords: puf, protein-rna complex, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Caenorhabditis elegans; More
• Total number of polymer chains: 6
• Total formula weight: 106096.28

Authors

Qiu, C.,Campbell, Z.T.,Hall, T.M.T. (deposition date: 2019-07-18, release date: 2019-08-21, Last modification date: 2023-10-11)

Primary citation

Qiu, C.,Bhat, V.D.,Rajeev, S.,Zhang, C.,Lasley, A.E.,Wine, R.N.,Campbell, Z.T.,Tanaka Hall, T.M.T.
A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity.
Elife, 8:-, 2019

PubMed Abstract: In the germline, 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 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.

PubMed: 31397673
DOI: 10.7554/eLife.48968

Experimental method

X-RAY DIFFRACTION (2.099 Å)