Human polypyrimidine-binding
splicing factor (PSF/SFPQ) is a
tumor suppressor protein that regulates the gene expression of several proto-oncogenes and binds to the 5'-polyuridine negative-sense template (5'-PUN) of some RNA viruses. The activity of PSF is negatively regulated by long-noncoding RNAs, human
metastasis associated in
lung adenocarcinoma transcript-1 and murine virus-like 30S transcript-1 (VL30-1). PSF is a 707-amino
acid protein that has
a DNA-binding domain and two RNA recognition motifs (RRMs). Although the structure of the apo-truncated PSF is known, how PSF recognizes
RNA remains elusive. Here, we report the 2.8 Å and 3.5 Å resolution crystal structures of a biologically active truncated construct of PSF (sPSF, consisting of residues 214-598) alone and in a complex with a 30mer fragment of VL30-1
RNA, respectively. The structure of the complex reveals how the 30mer
RNA is recognized at two U-specific induced-fit binding pockets, located at the previously unrecognized domain-swapped, inter-subunit RRM1 (of the first subunit)-RRM2 (of the second subunit) interfaces that do not exist in the apo structure. Thus, the sPSF dimer appears to have two conformations in
solution: one in a low-affinity state for
RNA binding, as seen in the apo-structure, and the other in a high-affinity state for
RNA binding, as seen in the sPSF-
RNA complex. PSF undergoes an all or nothing transition between having two or no
RNA-binding pockets. We predict that the
RNA binds with a high degree of positive cooperativity. These structures provide an insight into a new regulatory mechanism that is likely involved in promoting
malignancies and other human diseases.