SNAP output for PDB entry 3k5q [SNAP web server]

PDB-id

3k5q; SNAP-derived features in text and JSON formats; DNAproDB

Class

RNA-RNA binding protein

Method

X-ray (2.2 Å)

Summary

Crystal structure of fbf-2-fbe complex

Reference

Wang Y, Opperman L, Wickens M, Hall TM (2009): "Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein." Proc.Natl.Acad.Sci.USA, 106, 20186-20191. doi: 10.1073/pnas.0812076106.

Abstract

Caenorhabditis elegans fem-3 binding factor (FBF) is a founding member of the PUMILIO/FBF (PUF) family of mRNA regulatory proteins. It regulates multiple mRNAs critical for stem cell maintenance and germline development. Here, we report crystal structures of FBF in complex with 6 different 9-nt RNA sequences, including elements from 4 natural mRNAs. These structures reveal that FBF binds to conserved bases at positions 1-3 and 7-8. The key specificity determinant of FBF vs. other PUF proteins lies in positions 4-6. In FBF/RNA complexes, these bases stack directly with one another and turn away from the RNA-binding surface. A short region of FBF is sufficient to impart its unique specificity and lies directly opposite the flipped bases. We suggest that this region imposes a flattened curvature on the protein; hence, the requirement for the additional nucleotide. The principles of FBF/RNA recognition suggest a general mechanism by which PUF proteins recognize distinct families of RNAs yet exploit very nearly identical atomic contacts in doing so.