RNAs are one of the most challenging systems to study using conventional structural biology techniques. To address this challenge, we recently pioneered the use of cryogenic OrbiSIMS mass spectroscopy data in RNA folding and structure refinement algorithms to model native structures with atomic precision (Ward et al. 2024 Nat Comms). Through rigorous benchmarking against the existing high-resolution structures of prototypical systems available in the PDB, we have also thoroughly evaluated the accuracy, reliability, and limitations of our technique. Going beyond method development, by utilising the 7SK RNP as a test case, we have successfully unravelled the complete 3D structure of this native RNA in its apo and protein-bound forms, as well as in its disease-remodelled state. This comprehensive analysis provides unprecedented insights into the structural dynamics and interactions of the 7SK complex, with potential implications for understanding disease mechanisms.