Metazoan replication-dependent histone messenger RNAs (mRNAs) have a conserved stem-loop (SL) at their 3'-end. The stem-loop binding protein (SLBP) specifically recognizes the SL to regulate histone mRNA metabolism, and the 3'-5' exonuclease 3'hExo trims its 3'-end after processing. We report the crystal structure of a ternary complex of human SLBP RNA binding domain, human 3'hExo, and a 26-nucleotide SL RNA. Only one base of the SL is recognized specifically by SLBP, and the two proteins primarily recognize the shape of the RNA. SLBP and 3'hExo have no direct contact with each other, and induced structural changes in the loop of the SL mediate their cooperative binding. The 3' flanking sequence is positioned in the 3'hExo active site, but the ternary complex limits the extent of trimming.
Figure: Structure of human SLBP RBD, human 3'hExo, and SL RNA ternary complex. (A) Domain organizations of human SLBP and human 3'hExo. Residues not included in the expression constructs are shown in gray. (B) Schematic drawings of the structure of the ternary complex of human SLBP RBD (cyan), human 3.hExo (SAP domain in yellow and nuclease domain in green), and 26-nucleotide SL RNA (orange). (C) Simulated annealing omit Fobs - Fcalc electron density (light green) for the SL RNA at 2.6 å resolution, contoured at 3σ. Phosphorus atoms are in yellow, oxygens in red, and nitrogens in blue. (D) Close-up of the loop region of the SL RNA. All the structure figures were produced with PyMOL (www.pymol.org).
Tan D, Marzluff WF, Dominski Z, Tong L.
Structure of histone mRNA stem-loop, human stem-loop binding protein, and 3'hExo ternary complex.
Science. 2013 Jan 18;339(6117):318-21. doi: 10.1126/science.1228705.