De novo protein structure determination from near-atomic-resolution cryo-EM maps

Ray Yu-Ruei Wang; Mikhail Kudryashev; Xueming Li; Edward H Egelman; Marek Basler; Yifan Cheng; David Baker; Frank DiMaio

doi:10.1038/nmeth.3287

De novo protein structure determination from near-atomic-resolution cryo-EM maps

Nat Methods. 2015 Apr;12(4):335-8. doi: 10.1038/nmeth.3287. Epub 2015 Feb 23.

Authors

Ray Yu-Ruei Wang¹, Mikhail Kudryashev², Xueming Li³, Edward H Egelman⁴, Marek Basler⁵, Yifan Cheng³, David Baker⁶, Frank DiMaio⁷

Affiliations

¹ 1] Graduate program in Biological Physics, Structure and Design, University of Washington, Seattle, Washington, USA. [2] Department of Biochemistry, University of Washington, Seattle, Washington, USA.
² 1] Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland. [2] Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Basel, Switzerland.
³ The Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA.
⁴ Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA.
⁵ Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland.
⁶ 1] Department of Biochemistry, University of Washington, Seattle, Washington, USA. [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA.
⁷ Department of Biochemistry, University of Washington, Seattle, Washington, USA.

Abstract

We present a de novo model-building approach that combines predicted backbone conformations with side-chain fit to density to accurately assign sequence into density maps. This method yielded accurate models for six of nine experimental maps at 3.3- to 4.8-Å resolution and produced a nearly complete model for an unsolved map containing a 660-residue heterodimeric protein. This method should enable rapid and reliable protein structure determination from near-atomic-resolution cryo-electron microscopy (cryo-EM) maps.

Publication types

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

MeSH terms

Chemistry, Physical / methods*
Cryoelectron Microscopy*
Models, Molecular*
Monte Carlo Method
Protein Conformation
Proteins / chemistry*
Time Factors

Substances

Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding