1. Structural Biology and Molecular Biophysics

Model-based local density sharpening of cryo-EM maps

  1. Arjen J Jakobi
  2. Matthias Wilmanns
  3. Carsten Sachse  Is a corresponding author
  1. European Molecular Biology Laboratory, Germany
https://doi.org/10.7554/eLife.27131
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  1. Arjen J Jakobi
  2. Matthias Wilmanns
  3. Carsten Sachse
(2017)
Model-based local density sharpening of cryo-EM maps
eLife 6:e27131.
https://doi.org/10.7554/eLife.27131
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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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The following previously published data sets were used

Article and author information

Author details

  1. Arjen J Jakobi

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7761-2027

  2. Matthias Wilmanns

    European Molecular Biology Laboratory, Hamburg, Germany
    Competing interests
    The authors declare that no competing interests exist.

  3. Carsten Sachse

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    For correspondence
    carsten.sachse@embl.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1168-5143

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

  1. Axel T Brunger, Stanford University Medical Center, United States

Version history

  1. Received: March 23, 2017
  2. Accepted: October 22, 2017
  3. Accepted Manuscript published: October 23, 2017 (version 1)
  4. 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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  1. Arjen J Jakobi
  2. Matthias Wilmanns
  3. Carsten Sachse
(2017)
Model-based local density sharpening of cryo-EM maps
eLife 6:e27131.
https://doi.org/10.7554/eLife.27131

Share this article

https://doi.org/10.7554/eLife.27131

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