2’-O-rRNA methylation, which is essential in eukaryotes and archaea, is catalysed by the Box C/D RNP complex in an RNA-guided manner. Despite the conservation of the methylation sites, the abundance of site-specific modifications shows variability across species and tissues, suggesting that rRNA methylation may provide a means of controlling gene expression. As all Box C/D RNPs are thought to adopt a similar structure, it remains unclear how the methylation efficiency is regulated. Here, we provide the first structural evidence that, in the context of the Box C/D RNP, the affinity of the catalytic module fibrillarin for the substrate–guide helix is dependent on the RNA sequence outside the methylation site, thus providing a mechanism by which both the substrate and guide RNA sequences determine the degree of methylation. To reach this result, we develop an iterative structure calculation protocol that exploits the power of integrative structural biology to characterize conformational ensembles.

The dataset is linked to the following manuscript:

The dataset contains models and data underlying all figures and analysis in the manuscript.

The associated SASDB entries are:

SASDGV2, SASDGW2, SASDGX2, SASDGY2, SASDGZ2, SASDG23, SASDG33, SASDG43, SASDG53, SASDG63, SASDG73, SASDG83, SASDG93, SASDGA3

the Distance_restraints directory includes the binned distance restraints used for structure calculation with Aria/CNS2.1

the Representative_structures directory includes ensemble centroid models after Cartesian refinement and selection by consensus NMR/SAS.

.in files are AMBER input files with parameters of analysis of MD trajectories

.fit files are fits to experimental scattering curves to be opened with the ATSAS suite.