In this study, we used a combination of atomic force microscopy topography and the AFM-Assembly pipeline to reconstruct the pentameric structures of IgM Fc cores. These structures illustrate potential alternative orientations of the Cµ2-Cµ3 connection. Of particular significance is the finding that these alternative conformations were deduced from the experimental constraints of the AFM data. The conformational variability observed in our reconstruction may result from favorable convolution between the low resolution of AFM topography (including the tip effect) and the resolution of Cα-level atomic reconstruction in the assembly process. The dynamic view of the reconstructed IgM Fc core presented in this study contrasts with cryo-EM structures, which infer conformational variability through the absence of clearly defined densities. This work presents a novel perspective on the AFM-Assembly pipeline’s capability to provide a pseudo-dynamic representation of potential flexible molecular arrangements.
AFM imaging and reconstruction were performed by Harinderbir Kaur.