A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps

Thomas C Terwilliger; Paul D Adams; Pavel V Afonine; Oleg V Sobolev

doi:10.1038/s41592-018-0173-1

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps

Nat Methods. 2018 Nov;15(11):905-908. doi: 10.1038/s41592-018-0173-1. Epub 2018 Oct 30.

Authors

Thomas C Terwilliger^{1

2}, Paul D Adams^{3

4}, Pavel V Afonine^{3

5}, Oleg V Sobolev³

Affiliations

¹ Los Alamos National Laboratory, Los Alamos, NM, USA. [email protected].
² New Mexico Consortium, Los Alamos, NM, USA. [email protected].
³ Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
⁴ Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
⁵ Department of Physics and International Centre for Quantum and Molecular Structures, Shanghai University, Shanghai, China.

Abstract

We report a fully automated procedure for the optimization and interpretation of reconstructions from cryo-electron microscopy (cryo-EM) data, available in Phenix as phenix.map_to_model. We applied our approach to 476 datasets with resolution of 4.5 Å or better, including reconstructions of 47 ribosomes and 32 other protein-RNA complexes. The median fraction of residues in the deposited structures reproduced automatically was 71% for reconstructions determined at resolutions of 3 Å or better and 47% for those at resolutions worse than 3 Å.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Cryoelectron Microscopy / instrumentation
Cryoelectron Microscopy / methods*
Humans
Models, Molecular*
Protein Conformation
RNA / chemistry*
RNA / metabolism
RNA-Binding Proteins / chemistry*
RNA-Binding Proteins / metabolism
Ribosomes / chemistry*
Ribosomes / metabolism

Substances

RNA-Binding Proteins
RNA

Grants and funding

P01 GM063210/GM/NIGMS NIH HHS/United States