A Bayesian View on Cryo-EM Structure Determination

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.
Journal of Molecular Biology (Impact Factor: 4.33). 11/2011; 415(2):406-18. DOI: 10.1016/j.jmb.2011.11.010
Source: PubMed


Three-dimensional (3D) structure determination by single-particle analysis of cryo-electron microscopy (cryo-EM) images requires many parameters to be determined from extremely noisy data. This makes the method prone to overfitting, that is, when structures describe noise rather than signal, in particular near their resolution limit where noise levels are highest. Cryo-EM structures are typically filtered using ad hoc procedures to prevent overfitting, but the tuning of arbitrary parameters may lead to subjectivity in the results. I describe a Bayesian interpretation of cryo-EM structure determination, where smoothness in the reconstructed density is imposed through a Gaussian prior in the Fourier domain. The statistical framework dictates how data and prior knowledge should be combined, so that the optimal 3D linear filter is obtained without the need for arbitrariness and objective resolution estimates may be obtained. Application to experimental data indicates that the statistical approach yields more reliable structures than existing methods and is capable of detecting smaller classes in data sets that contain multiple different structures.

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    • "Relion version 1.2 was used for final refinement, resulting in a final 21-Å resolution structure (judging by the Fourier shell correlation [FSC] cutoff of 0.5) that clearly shows a ridge of density at the beak to hold it in the retracted position (Fig. 2 A and Fig. S1 B). Further multimodel 3D refinement and CTF correction in Relion (Scheres, 2012), which allows the data to separate into two distinct "
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    • "Finally, 219,169 and 160,264 particles, for low salt and high salt intermediates, respectively, were kept and subjected to single particle analysis. To explore the structural heterogeneity , classification was applied both at two dimensional (2D) and three dimensional (3D) levels, using RELION, an empirical Bayesian approach (Scheres, 2012). Both samples were first classified into 200 classes at 2D level in 25 iterations with an angle step of 5 degree, and bad particles were excluded from further analysis. "
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    Protein & Cell 03/2014; 5(5). DOI:10.1007/s13238-014-0044-1 · 3.25 Impact Factor
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    • "It resulted in a 9.1-Å structure [gold standard Fourier shell correlation (FSC) = 0.143] showing fragmented densities in the intersubunit space, indicative of heterogeneity. The data set was then subjected to RELION classification (28) starting with 10 classes (k = 10). Of the 10 classes, class 8 (Figure 1) was well populated (48 973 particles, 25.1%), with well-defined additional masses of density in the intersubunit space corresponding to eRF1, eRF3 and P-site tRNA as previously described (26). "
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