Improved Accuracy from Joint X‑ray and NMR Refinement of a Protein–RNA Complex Structure

Integrated experimental approaches
play an increasingly important
role in structural biology, taking advantage of the complementary
information provided by different techniques. In particular, the combination
of NMR data with X-ray diffraction patterns may provide accurate and
precise information about local conformations not available from average-resolution
X-ray structures alone. Here, we refined the structure of a ternary
protein–protein–RNA complex comprising three domains,
Sxl and Unr, bound to a single-stranded region derived in the msl2 mRNA. The joint X-ray and NMR refinement reveals thatdespite
the poor quality of the fit found for the original structural modelthe
NMR data can be largely accommodated within the uncertainty in the
atom positioning (structural noise) from the primary X-ray data and
that the overall domain arrangements and binding interfaces are preserved
on passing from the crystalline state to the solution. The refinement
highlights local conformational differences, which provide additional
information on specific features of the structure. For example, conformational
dynamics and heterogeneity observed at the interface between the CSD1
and the Sxl protein components in the ternary complex are revealed
by the combination of NMR and crystallographic data. The joint refinement
protocol offers unique opportunities to detect structural differences
arising from various experimental conditions and reveals static or
dynamic differences in the conformation of the biomolecule between
the solution and the crystals.