E0073: Structural Characterization of a Universally Conserved Protein-RNA Interaction from the Signal Recognition Particle

In cells, proteins are targeted to for secretion or insertion into the cell membrane with the aid of the signal recognition particle (SRP), a ubiquitous ribonucleoprotein complex. The interaction between the signal sequence recognition protein, SRP54/Ffh and the SRP RNA is mediatied by the universally conserved M-domain. To understand this recognition, an RNA-protein complex was crystallized, resulting in a crystal that diffract x-rays to 1.52 Å resolution. The phase problem was solved using the multiple wavelength anomalous diffraction (MAD) method with crystals containing selenomethionine labeled protein. From this data, a model of the complex is being constructed that currently includes diffraction data to 1.8 Å and has a crystallographic R-factor of 19.9% and a free R-factor of 22.1%. Strikingly, all of the amino acids within the M-domain and nucleotides in the 4.5S RNA that are at the molecular interface are universally conserved across all three kingdoms of life. This interface comprises two of the four principal alpha helices in the M-domain docking into the minor groove of a symmetric internal loop in the 4.5S RNA. Within this loop are several unusual base pairing schemes that have not been previously observed, including a sheared G-G pair and a "pair of pairs". Additionally, the asymmetric internal loop bulges out from the RNA to create a series of stacked nucleotides, whose penultimate adenosine base is extensively recognized by the protein. These two internal loops are connected by a universally conserved salt bridge within the M-domain and by a tertiary contact within the ribose-phosphate backbone. This structure also reveals a number of well-ordered potassium and magnesium ions as well as water molecules that appear to make significant contributions to the stabilization of the complex.