Model-based local density sharpening of cryo-EM maps
- European Molecular Biology Laboratory, Germany
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.
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Author details
Funding
Marie Curie Actions (PCOFUND-GA-2008-229597)
- Arjen J Jakobi
Marie-Sklodowska-Curie (PIEF-GA-2012-331285)
- Arjen J Jakobi
Deutsche Forschungsgemeinschaft (Hamburg Center for Ultrafast Imaging (CUI))
- Arjen J Jakobi
Joachim Herz Stiftung
- Arjen J Jakobi
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Axel T Brunger, Stanford University Medical Center, United States
Version history
- Received: March 23, 2017
- Accepted: October 22, 2017
- Accepted Manuscript published: October 23, 2017 (version 1)
- Version of Record published: November 9, 2017 (version 2)
Copyright
© 2017, Jakobi et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Model-based local density sharpening of cryo-EM maps
eLife 6:e27131.
https://doi.org/10.7554/eLife.27131
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