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

Abstract
Data availability
Article and author information
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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

1. Liao M
2. Cao E
3. Julius D
4. Cheng Y
(2013) Structure of the capsaicin receptor, TRPV1, determined by single particle electron cryo-microscopy
EMD-5778.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-5778
(2014) Electron cryo-microscopy of F420-reducing [NiFe] hydrogenase Frh
EMD-2513.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-2513/
1. Brown A
2. Amunts A
3. Bai XC
4. Sugimoto Y
5. Edwards PC
6. Murshudov G
7. Scheres SHW
8. Ramakrishnan V
(2014) Electron cryo-microscopy of human mitochondrial large ribosomal subunit
EMD-2762.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-2762

Article and author information

Author details

Ray Yu-Ruei Wang

Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0001-5025-9596
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.
Benjamin A Barad

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-1016-862X
Yifan Cheng

Keck Advanced Microscopy Laboratory, University of California, San Francisco, San Francisco, United States

Competing interests
No competing interests declared.
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.

"This ORCID iD identifies the author of this article:" 0000-0002-5080-2859
Frank DiMaio

Department of Biochemistry, University of Washington, Seattle, United States

For correspondence
dimaio@uw.edu

Competing interests
No competing interests declared.

"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.

Copyright

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.