Summary information and primary citation

PDB-id
3k64; DSSR-derived features in text and JSON formats
Class
RNA-RNA binding protein
Method
X-ray (2.0 Å)
Summary
Crystal structure of fbf-2-fem-3 pme 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.

Cartoon-block schematics in six views (download the tarball)

PyMOL session file Download PDB file View in 3Dmol.js