Abstract of the PDB Structure's related Publication:
Box C/D small nucleolar and Cajal body ribonucleoprotein particles (sno/scaRNPs) direct site-specific 2'-O-methylation of ribosomal and spliceosomal RNAs and are critical for gene expression. Here we report crystal structures of an archaeal box C/D RNP containing three core proteins (fibrillarin, Nop56/58, and L7Ae) and a half-mer box C/D guide RNA paired with a substrate RNA. The structure reveals a guide-substrate RNA duplex orientation imposed by a composite protein surface and the conserved GAEK motif of Nop56/58. Molecular modeling supports a dual C/D RNP structure that closely mimics that recently visualized by electron microscopy. The substrate-bound dual RNP model predicts an asymmetric protein distribution between the RNP that binds and methylates the substrate RNA. The predicted asymmetric nature of the holoenzyme is consistent with previous biochemical data on RNP assembly and provides a simple solution for accommodating base-pairing between the C/D guide RNA and large ribosomal and spliceosomal substrate RNAs.
L7Ae protein, together with fused Nop56/58 (also designated Nop5) and Fibrillarin methyltranferase (FlpA), makes the core of C/D RNP complex in Archaea. It is a homologue of S. cerevisiae Snu13 and mammalian 15.5kD protein. Archaeal L7Ae is also a subunit of H/ACA RNP complex, a subunit of RNase P and one of the ribosomal protein of the 50S subunit. In all cases L7Ae binds to a common kink-turn motif of RNA.