Beam-induced motion correction for sub-megadalton cryo-EM particles
Tóm tắt
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.
Từ khóa
Tài liệu tham khảo
Allegretti, 2014, Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector, eLife, 3, e01963, 10.7554/eLife.01963
Amunts, 2014, Structure of the yeast mitochondrial large ribosomal subunit, Science, 343, 1485, 10.1126/science.1249410
Bai, 2013, Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles, eLife, 2, e00461, 10.7554/eLife.00461
Brilot, 2012, Beam-induced motion of vitrified specimen on holey carbon film, Journal of Structural Biology, 177, 630, 10.1016/j.jsb.2012.02.003
Campbell, 2012, Movies of ice-embedded particles enhance resolution in electron cryo-microscopy, Structure, 20, 1823, 10.1016/j.str.2012.08.026
Chen, 2013, High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy, Ultramicroscopy, 135, 24, 10.1016/j.ultramic.2013.06.004
Glaeser, 2011, Reaching the information limit in cryo-EM of biological macromolecules: experimental aspects, Biophysical Journal, 100, 2331, 10.1016/j.bpj.2011.04.018
Hayward, 1979, Radiation damage of purple membrane at low temperature, Ultramicroscopy, 04, 201, 10.1016/S0304-3991(79)90211-0
Li, 2013, Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM, Nature Methods, 10, 584, 10.1038/nmeth.2472
Liao, 2013, Structure of the TRPV1 ion channel determined by electron cryo-microscopy, Nature, 504, 107, 10.1038/nature12822
McMullan, 2009, Experimental observation of the improvement in MTF from backthinning a CMOS direct electron detector, Ultramicroscopy, 109, 1144, 10.1016/j.ultramic.2009.05.005
Mindell, 2003, Accurate determination of local defocus and specimen tilt in electron microscopy, Journal of Structural Biology, 142, 334, 10.1016/S1047-8477(03)00069-8
Pettersen, 2004, UCSF Chimera–a visualization system for exploratory research and analysis, Journal of Computational Chemistry, 25, 1605, 10.1002/jcc.20084
Rosenthal, 2003, Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy, Journal of Molecular Biology, 333, 721, 10.1016/j.jmb.2003.07.013
Russo, 2014, Controlling protein adsorption on graphene for cryo-EM using low-energy hydrogen plasmas, Nature Methods, 11, 649, 10.1038/nmeth.2931
Scheres, 2012, RELION: implementation of a Bayesian approach to cryo-EM structure determination, Journal of Structural Biology, 180, 519, 10.1016/j.jsb.2012.09.006
Scheres, 2012, Prevention of overfitting in cryo-EM structure determination, Nature Methods, 9, 853, 10.1038/nmeth.2115
Stark, 1996, Electron radiation damage to protein crystals of bacteriorhodopsin at different temperatures, Ultramicroscopy, 63, 75, 10.1016/0304-3991(96)00045-9
Tang, 2007, EMAN2: an extensible image processing suite for electron microscopy, Journal of Structural Biology, 157, 38, 10.1016/j.jsb.2006.05.009
Unwin, 1975, Molecular structure determination by electron microscopy of unstained crystalline specimens, Journal of Molecular Biology, 94, 425, 10.1016/0022-2836(75)90212-0
Vinothkumar, 2014a, Molecular mechanism of antibody-mediated activation of β-galactosidase, Structure, 22, 621, 10.1016/j.str.2014.01.011