DOI: 10.7554/elife.03665. Beam-induced motion correction for sub-megadalton cryo-EM particles

Beam-induced motion correction for sub-megadalton cryo-EM particles

10.7554/elife.03665

Crossref journal-article

eLife Sciences Publications, Ltd

eLife (4374)

Abstract

In electron cryo-microscopy (cryo-EM), the electron beam that is used for imaging also causes the sample to move. This motion blurs the images and limits the resolution attainable by single-particle analysis. In a previous Research article (<xref ref-type="bibr" rid="bib3">Bai et al., 2013</xref>) we showed that correcting for this motion by processing movies from fast direct-electron detectors allowed structure determination to near-atomic resolution from 35,000 ribosome particles. In this Research advance article, we show that an improved movie processing algorithm is applicable to a much wider range of specimens. The new algorithm estimates straight movement tracks by considering multiple particles that are close to each other in the field of view, and models the fall-off of high-resolution information content by radiation damage in a dose-dependent manner. Application of the new algorithm to four data sets illustrates its potential for significantly improving cryo-EM structures, even for particles that are smaller than 200 kDa.

Bibliography

Scheres, S. H. (2014). Beam-induced motion correction for sub-megadalton cryo-EM particles. ELife, 3. CLOCKSS.

Authors 1

Sjors HW Scheres (first)

References 24 Referenced 305

10.7554/eLife.01963 / eLife / Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector by Allegretti (2014)
10.1126/science.1249410 / Science / Structure of the yeast mitochondrial large ribosomal subunit by Amunts (2014)
10.7554/eLife.00461 / eLife / Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles by Bai (2013)
10.1016/j.jsb.2012.02.003 / Journal of Structural Biology / Beam-induced motion of vitrified specimen on holey carbon film by Brilot (2012)
10.1016/j.str.2012.08.026 / Structure / Movies of ice-embedded particles enhance resolution in electron cryo-microscopy by Campbell (2012)
10.1016/j.ultramic.2013.06.004 / Ultramicroscopy / High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy by Chen (2013)
10.1016/j.bpj.2011.04.018 / Biophysical Journal / Reaching the information limit in cryo-EM of biological macromolecules: experimental aspects by Glaeser (2011)
10.1016/S0304-3991(79)90211-0 / Ultramicroscopy / Radiation damage of purple membrane at low temperature by Hayward (1979)
10.1038/nmeth.2472 / Nature Methods / Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM by Li (2013)
10.1038/nature12822 / Nature / Structure of the TRPV1 ion channel determined by electron cryo-microscopy by Liao (2013)
10.1038/nature13567 / Nature / Three-dimensional structure of human γ-secretase by Lu (2014)
10.1016/j.ultramic.2009.05.005 / Ultramicroscopy / Experimental observation of the improvement in MTF from backthinning a CMOS direct electron detector by McMullan (2009)
10.1016/S1047-8477(03)00069-8 / Journal of Structural Biology / Accurate determination of local defocus and specimen tilt in electron microscopy by Mindell (2003)
10.1002/jcc.20084 / Journal of Computational Chemistry / UCSF Chimera–a visualization system for exploratory research and analysis by Pettersen (2004)
10.1016/j.jmb.2003.07.013 / Journal of Molecular Biology / Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy by Rosenthal (2003)
10.1038/nmeth.2931 / Nature Methods / Controlling protein adsorption on graphene for cryo-EM using low-energy hydrogen plasmas by Russo (2014)
10.1016/j.jsb.2012.09.006 / Journal of Structural Biology / RELION: implementation of a Bayesian approach to cryo-EM structure determination by Scheres (2012)
10.1038/nmeth.2115 / Nature Methods / Prevention of overfitting in cryo-EM structure determination by Scheres (2012)
10.1016/0304-3991(96)00045-9 / Ultramicroscopy / Electron radiation damage to protein crystals of bacteriorhodopsin at different temperatures by Stark (1996)
10.1016/j.jsb.2006.05.009 / Journal of Structural Biology / EMAN2: an extensible image processing suite for electron microscopy by Tang (2007)
10.1016/0022-2836(75)90212-0 / Journal of Molecular Biology / Molecular structure determination by electron microscopy of unstained crystalline specimens by Unwin (1975)
10.1016/j.str.2014.01.011 / Structure / Molecular mechanism of antibody-mediated activation of β-galactosidase by Vinothkumar (2014a)
10.1038/nature13686 / Nature / Architecture of mammalian respiratory complex I by Vinothkumar (2014b)
10.7554/eLife.03080 / eLife / Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine by Wong (2014)

Dates

Type	When
Created	11 years ago (Aug. 12, 2014, 10:37 a.m.)
Deposited	1 year, 10 months ago (Oct. 11, 2023, 8:47 p.m.)
Indexed	1 week ago (Aug. 23, 2025, 1:11 a.m.)
Issued	11 years ago (Aug. 13, 2014)
Published	11 years ago (Aug. 13, 2014)
Published Online	11 years ago (Aug. 13, 2014)

Funders 2

Medical Research Council 10.13039/501100000265
Region: Europe
gov (National government)
Labels3
1. Medical Research Council (United Kingdom)
2. UK Medical Research Council
3. MRC
Awards1
1. MC_UP_A025_1012
Medical Research Council 10.13039/501100000265
Region: Europe
gov (National government)
Labels3
1. Medical Research Council (United Kingdom)
2. UK Medical Research Council
3. MRC
Awards1
1. MC_UP_A025_1012

BibTeX

@article{Scheres_2014, title={Beam-induced motion correction for sub-megadalton cryo-EM particles}, volume={3}, ISSN={2050-084X}, url={http://dx.doi.org/10.7554/elife.03665}, DOI={10.7554/elife.03665}, journal={eLife}, publisher={eLife Sciences Publications, Ltd}, author={Scheres, Sjors HW}, year={2014}, month=aug }

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