Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

  1. Ray Yu-Ruei Wang
  2. Yifan Song
  3. Benjamin A Barad
  4. Yifan Cheng
  5. James S Fraser
  6. Frank DiMaio  Is a corresponding author
  1. University of California, San Francisco, United States
  2. Cyrus Biotechnology, United States
  3. University of Washington, United States

Abstract

Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids - typical in a macromolecular assembly - is tedious and time-consuming. We present an automated method that can improve the atomic details in models manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps.

Data availability

The following previously published data sets were used

Article and author information

Author details

  1. Ray Yu-Ruei Wang

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5025-9596
  2. Yifan Song

    Cyrus Biotechnology, Seattle, United States
    Competing interests
    Yifan Song, Co-founder of Cyrus Biotechnology, Inc., which will develop and market graphic-interface software for using Rosetta.
  3. Benjamin A Barad

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1016-862X
  4. Yifan Cheng

    Keck Advanced Microscopy Laboratory, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
  5. James S Fraser

    Department of Bioengineering and Therapeutic Science, California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5080-2859
  6. Frank DiMaio

    Department of Biochemistry, University of Washington, Seattle, United States
    For correspondence
    dimaio@uw.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7524-8938

Funding

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, Howard Hughes Medical Institute, Stanford University, United States

Publication history

  1. Received: April 26, 2016
  2. Accepted: September 22, 2016
  3. Accepted Manuscript published: September 26, 2016 (version 1)
  4. Version of Record published: November 18, 2016 (version 2)

Copyright

© 2016, Wang 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. Ray Yu-Ruei Wang
  2. Yifan Song
  3. Benjamin A Barad
  4. Yifan Cheng
  5. James S Fraser
  6. Frank DiMaio
(2016)
Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta
eLife 5:e17219.
https://doi.org/10.7554/eLife.17219

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