Cryo-electron microscopy (cryo-EM) coupled to single particle analysis is an important technique for determining the structure of isolated proteins and protein complexes. A key step in the procedure is three-dimensional reconstruction in which individual two-dimensional molecular images in different orientations are combined to produce the final three-dimensional reconstruction. Here we describe a new computer program, icr3d, which carries out this step by merging the input data in Fourier space. This is achieved by calculating a weighted average of the input data for each Fourier component of the final three-dimensional map. Weighting factors are used to take account of the contrast transfer function of the input data and the interpolation onto the required three-dimensional grid. The latter step uses a sinc function scaled to the fractional spatial occupancy of the target structure within the reconstructed volume. The program has been used in recent high resolution cryo-EM studies (da Fonseca and Morris, 2015, Li et al, 2016) and is freely available for download as part of the tigris package for image analysis of cryo-EM data at sourceforge.net.
References
da Fonseca, P. C. & Morris, E. P. (2015). Cryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core. Nat Commun 6, 7573.
Li, H., O’Donoghue, A. J., van der Linden, W. A., Xie, S. C., Yoo, E., Foe, I. T., Tilley, L., Craik, C. S., da Fonseca, P. C. A. & Bogyo, M. (2016). Structure- and function-based design of Plasmodium-selective proteasome inhibitors. Nature 530, 233-236.
