Model-based local density sharpening of cryo-EM maps.

Arjen J Jakobi,Matthias Wilmanns,Carsten Sachse

doi:10.7554/elife.27131

Abstract

Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Here, we introduce a general procedure for local sharpening of cryo-EM density maps based on prior knowledge of an atomic reference structure. The procedure optimizes contrast of cryo-EM densities by amplitude scaling against the radially averaged local falloff estimated from a windowed reference model. By testing the procedure using six cryo-EM structures of TRPV1, β-galactosidase, γ-secretase, ribosome-EF-Tu complex, 20S proteasome and RNA polymerase III, we illustrate how local sharpening can increase interpretability of density maps in particular in cases of resolution variation and facilitates model building and atomic model refinement.

Highlights

Electron cryo-microscopy has been used as a method to visualize biological macromolecules in their native-hydrated state for more than three decades (Adrian et al, 1984)
Based on several test cases from the EMDB model challenge, we show that model-based local sharpening can facilitate model building and refinement by increasing local density contrast
We have introduced a procedure to improve the interpretability of cryo-EM density maps by modelbased local sharpening

Summary

Introduction

Electron cryo-microscopy (cryo-EM) has been used as a method to visualize biological macromolecules in their native-hydrated state for more than three decades (Adrian et al, 1984). Major improvements in detector technology (Faruqi and Henderson, 2007; McMullan et al, 2016) and associated computational procedures recently transformed single-particle cryo-EM that since has been producing a plenitude of near-atomic resolution structures from specimens of lower symmetry (Allegretti et al, 2014; Amunts et al, 2014; Bai et al, 2013) and lower molecular weight than previously deemed possible (Bai et al, 2015; Liao et al, 2013; Merk et al, 2016) At this resolution, the reconstructed EM density maps contain sufficient detail to interpret the structure using atomic models. The cryo-EM experiment yields both amplitudes and phases directly from images and experimentally determined EM density can be used as a constant minimization target (Grigorieff et al, 1996; Unwin, 2005; Yonekura et al, 2003)

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