Measuring the effects of particle orientation to improve the efficiency of electron cryomicroscopy

Nature Communications

Volumn 8, Issue 1, 2017, Pages

  Naydenova, Katerina ^a,b   Russo, Christopher J ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^b TRINITY COLLEGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DENSITY; ELECTRON MICROSCOPY; ORIENTATION; RECONSTRUCTION; RESOLUTION; SAMPLE PREPARATION; STATISTICAL ANALYSIS;

CRYOELECTRON MICROSCOPY; HUMAN; HUMAN TISSUE; ALGORITHM; FOURIER ANALYSIS; PROCEDURES; PRODUCTIVITY; RIBOSOMAL SUBUNIT; SOFTWARE; SPATIAL ORIENTATION; SPECIMEN HANDLING; THREE DIMENSIONAL IMAGING; ULTRASTRUCTURE;

ALGORITHMS; CRYOELECTRON MICROSCOPY; EFFICIENCY; FOURIER ANALYSIS; IMAGING, THREE-DIMENSIONAL; ORIENTATION, SPATIAL; RIBOSOME SUBUNITS; SOFTWARE; SPECIMEN HANDLING;

EID: 85029639811     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/s41467-017-00782-3     Document Type: Article

References (26)

1. Cheng, Y. Single-particle cryo-EM at crystallographic resolution. Cell 161, 450-457 (2015).
2. Fernandez-Leiro, R. & Scheres, S. H. W. Unravelling biological macromolecules with cryo-electron microscopy. Nature 537, 339-346 (2016)
3. Frank, J. Advances in the field of single-particle cryo-electron microscopy over the last decade. Nat. Protoc. 12, 209-212 (2017).
4. Russo, C. J. & Passmore, L. A. Progress towards an optimal specimen support for electron cryomicroscopy. Curr. Opin. Struct. Biol. 37, 81-89 (2016).
5. Glaeser, R. M. & Han, B.-G. Opinion: hazards faced by macromolecules when confined to thin aqueous films. Biophys. Rep. 3, 1-7 (2016).
6. Radermacher, M. Three-dimensional reconstruction of single particles from random and nonrandom tilt series. J. Electron. Microsc. Tech. 9, 359-394 (1988).
7. Henderson, R., Baldwin, J. M. & Ceska, T. Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J. Mol. Biol. 213, 899-929 (1990).
8. Diebolder, C. A., Faas, F. G., Koster, A. J. & Koning, R. I. Conical Fourier shell correlation applied to electron tomograms. J. Struct. Biol. 190, 215-223 (2015).
9. Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721-745 (2003).
10. Agard, D. A., Hiraoka, Y. & Sedat, J. W. Three-dimensional microscopy: image processing for high-resolution subcellular imaging. SPIE New Methods Microsc. Low Light Imaging 1161, 24-30 (1989).
11. Grigorieff, N. Frealign: an exploratory tool for single-particle cryo-EM. Methods Enzymol. 579, 191-226 (2016).
12. Ludtke, S. J. Single-particle refinement and variability analysis in EMAN2.1. Methods Enzymol. 579, 159-189 (2016).
13. Scheres, S. H. W. Processing of structurally heterogeneous cryo-EM data in RELION. Methods Enzymol. 579, 125-157 (2016).
14. Vinothkumar, K. R., McMullan, G. & Henderson, R. Molecular mechanism of antibody-mediated activation of ?-galactosidase. Structure 22, 621-627 (2014).
15. Campbell, M. G., Veesler, D., Cheng, A., Potter, C. S. & Carragher, B. 2.8 Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy. eLife 4, e06380 (2015)
16. Bai, X.-C., Fernandez, I. S., McMullan, G. & Scheres, S. H. W. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles. eLife 2, e00461 (2013).
17. Russo, C. J. & Passmore, L. A. Controlling protein adsorption on graphene for cryo-EM using low-energy hydrogen plasmas. Nat. Methods 11, 773-773 (2014).
18. Kucukelbir, A., Sigworth, F. J. & Tagare, H. D. Quantifying the local resolution of cryo-EM density maps. Nat. Methods 11, 63-65 (2014).
19. Rosenthal, P. B. Testing the validity of single-particle maps at low and high resolution. Methods Enzymol. 579, 227-253 (2016).
20. Frigo, M. & Johnson, S. G. The design and implementation of FFTW3. Proc. IEEE 93, 216-231 (2005).
21. Cheng, A. et al. MRC2014: extensions to the MRC format header for electron cryo-microscopy and tomography. J. Struct. Biol. 192, 146-150 (2015).
22. Elmlund, D. & Elmlund, H. SIMPLE: software for ab initio reconstruction of heterogeneous single-particles. J. Struct. Biol. 180, 420-427 (2012).
23. Elmlund, H., Elmlund, D. & Bengio, S. PRIME: probabilistic initial 3D model generation for single-particle cryo-electron microscopy. Structure 21, 1299-1306 (2013).
24. Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. J. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290-296 (2017).
25. Sorzano, C. et al. XMIPP: a new generation of an open-source image processing package for electron microscopy. J. Struct. Biol. 148, 194-204 (2004).
26. Russo, C. J. & Passmore, L. A. Ultrastable gold substrates for electron cryomicroscopy. Science 346, 1377-1380 (2014).