Molecular basis of sequence-specific recognition of pre-ribosomal RNA by nucleolin

The structure of the 28 kDa complex of the first two RNA binding domains (R BDs) of nucleolin (RBD12) with an RNA stem-loop that includes the nucleolin recognition element UCCCGA in the loop was determined by NMR spectroscopy. The structure of nucleolin RBD12 with the nucleolin recognition element (N RE) reveals that the two RBDs bind on opposite sides of the RNA loop, formi ng a molecular clamp that brings the 5' and 3' ends of the recognition sequ ence close together and stabilizing the stem-loop. The specific interaction s observed in the structure explain the sequence specificity for the NRE se quence. Binding studies of mutant proteins and analysis of conserved residu es support the proposed interactions. The mode of interaction of the protei n with the RNA and the location of the putative NRE sites suggest that nucl eolin may function as an RNA chaperone to prevent improper folding of the n ascent pre-rRNA.