Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.
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 that are 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 that 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.
Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, United States.|Department of Biochemistry, University of Washington, Seattle, United States.
Ray Yu-Ruei
0000-0001-5025-9596
RY
Wang
Department of Biochemistry, University of Washington, Seattle, United States.
Yifan
Y
Song
Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, United States.|Graduate Group in Biophysics, University of California, San Francisco, San Francisco, United States.
Benjamin A
0000-0002-1016-862X
BA
Barad
Keck Advanced Microscopy Laboratory, University of California, San Francisco, San Francisco, United States.|Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.
Yifan
Y
Cheng
Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, United States.
James S
0000-0002-5080-2859
JS
Fraser
Department of Biochemistry, University of Washington, Seattle, United States.|Institute for Protein Design, University of Washington, Seattle, United States.
Frank
0000-0002-7524-8938
F
DiMaio
D057205:Automation, Laboratory / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D020285:Cryoelectron Microscopy / Q000379:methods*; D046911:Macromolecular Substances / Q000648:ultrastructure*
D046911:Macromolecular Substances
Rosetta; atomic models; biophysics; computational biology; cryo-EM; macromolecular assemblies; membrane proteins; none; structural biology; structure refinement; systems biology
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