Single-Particle Refinement and Variability Analysis in EMAN2.1

Methods in Enzymology

Volumn 579, Issue , 2016, Pages 159-189

  Ludtke, S J ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

3 D reconstruction; CryoEM; EMAN; Heterogeneity; Image processing; Motion; Single particle analysis; Structural biology; Structural variability

Indexed keywords

ACCURACY; ANALYSIS OF VARIANCE; ELECTRON; EMAN2.1; IMAGE PROCESSING; IMAGE QUALITY; MAXIMUM LIKELIHOOD METHOD; PRINCIPAL COMPONENT ANALYSIS; PROTEIN QUATERNARY STRUCTURE; RIBOSOME; SOFTWARE; VALIDATION PROCESS; WORKFLOW; X RAY CRYSTALLOGRAPHY; ALGORITHM; ARTIFACT; CRYOELECTRON MICROSCOPY; DEVICES; MOTION; PROCEDURES; STATISTICS AND NUMERICAL DATA; THREE DIMENSIONAL IMAGING; ULTRASTRUCTURE;

BACTERIAL PROTEIN; CHAPERONIN 60;

ALGORITHMS; ANALYSIS OF VARIANCE; ARTIFACTS; BACTERIAL PROTEINS; CHAPERONIN 60; CRYOELECTRON MICROSCOPY; IMAGE PROCESSING, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; MOTION; RIBOSOMES; SOFTWARE;

EID: 85013784291     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/bs.mie.2016.05.001     Document Type: Chapter

References (47)

1. Bell, J.M., Chen, M., Baldwin, P.R., Ludtke, S.J., High resolution single particle refinement in EMAN2.1. Methods 100 (2016), 25–34.
2. Bharat, T.A., Russo, C.J., Löwe, J., Passmore, L.A., Scheres, S.H., Advances in single-particle electron cryomicroscopy structure determination applied to sub-tomogram averaging. Structure (London, England: 1993) 23:9 (2015), 1743–1753.
3. Braig, K., Otwinowski, Z., Hegde, R., Boisvert, D.C., Joachimiak, A., Horwich, A.L., et al. The crystal structure of the bacterial chaperonin GroEL at 2.8 Å. Nature 371:6498 (1994), 578–586.
4. Brignole, E.J., Smith, S., Asturias, F.J., Conformational flexibility of metazoan fatty acid synthase enables catalysis. Nature Structural & Molecular Biology 16:2 (2009), 190–197.
5. Brink, J., Ludtke, S.J., Kong, Y., Wakil, S.J., Ma, J., Chiu, W., Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis. Structure (London, England: 1993) 12:2 (2004), 185–191.
6. Chang, J.T., Schmid, M.F., Rixon, F.J., Chiu, W., Electron cryotomography reveals the portal in the herpesvirus capsid. Journal of Virology 81:4 (2007), 2065–2068.
7. Chaudhry, C., Horwich, A.L., Brunger, A.T., Adams, P.D., Exploring the structural dynamics of the E. coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states. Journal of Molecular Biology 342:1 (2004), 229–245.
8. Chen, D.H., Luke, K., Zhang, J., Chiu, W., Wittung-Stafshede, P., Location and flexibility of the unique C-terminal tail of Aquifex aeolicus co-chaperonin protein 10 as derived by cryo-electron microscopy and biophysical techniques. Journal of Molecular Biology 381:3 (2008), 707–717.
9. Chen, D.H., Song, J.L., Chuang, D.T., Chiu, W., Ludtke, S.J., An expanded conformation of single-ring GroEL-GroES complex encapsulates an 86 kDa substrate. Structure (London, England: 1993) 14:11 (2006), 1711–1722.
10. Cong, Y., Baker, M.L., Jakana, J., Woolford, D., Miller, E.J., Reissmann, S., et al. 4.0-Å resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement. Proceedings of the National Academy of Sciences of the United States of America 107:11 (2010), 4967–4972.
11. de la Rosa-Trevín, J.M., Otón, J., Marabini, R., Zaldívar, A., Vargas, J., Carazo, J.M., et al. Xmipp 3.0: An improved software suite for image processing in electron microscopy. Journal of Structural Biology 184:2 (2013), 321–328.
12. DiMaio, F., Zhang, J., Chiu, W., Baker, D., Cryo-EM model validation using independent map reconstructions. Protein Science: A Publication of the Protein Society 22:6 (2013), 865–868.
13. Frank, J., Agrawal, R.K., A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature 406:6793 (2000), 318–322.
14. Frank, J., Bretaudiere, J.P., Carazo, J.M., Verschoor, A., Wagenknecht, T., Classification of images of biomolecular assemblies: A study of ribosomes and ribosomal subunits of escherichia coli. Journal of Microscopy 150:Pt. 2 (1988), 99–115.
15. Frank, J., Radermacher, M., Penczek, P., Zhu, J., Li, Y., Ladjadj, M., et al. SPIDER and WEB: Processing and visualization of images in 3D electron microscopy and related fields. Journal of Structural Biology 116:1 (1996), 190–199.
16. Galaz-Montoya, J.G., Flanagan, J., Schmid, M.F., Ludtke, S.J., Single particle tomography in EMAN2. Journal of Structural Biology 190:3 (2015), 279–290.
17. Glaeser, R.M., Han, B.G., Csencsits, R., Killilea, A., Pulk, A., Cate, J.H., Factors that influence the formation and stability of thin, cryo-EM specimens. Biophysical Journal 110:4 (2016), 749–755.
18. Goddard, T.D., Huang, C.C., Ferrin, T.E., Visualizing density maps with UCSF chimera. Journal of Structural Biology 157:1 (2007), 281–287.
19. Grigorieff, N., FREALIGN: High-resolution refinement of single particle structures. Journal of Structural Biology 157:1 (2007), 117–125.
20. Henderson, R., The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules. Quarterly Reviews of Biophysics 28:2 (1995), 171–193.
21. Henderson, R., Sali, A., Baker, M.L., Carragher, B., Devkota, B., Downing, K.H., et al. Outcome of the first electron microscopy validation task force meeting. Structure (London, England: 1993) 20:2 (2012), 205–214.
22. Hohn, M., Tang, G., Goodyear, G., Baldwin, P.R., Huang, Z., Penczek, P.A., et al. SPARX, a new environment for cryo-EM image processing. Journal of Structural Biology 157:1 (2007), 47–55.
23. Lawson, C.L., Patwardhan, A., Baker, M.L., Hryc, C., Garcia, E.S., Hudson, B.P., et al. EMDataBank unified data resource for 3DEM. Nucleic Acids Research 44:D1 (2016), D396–D403, 10.1093/nar/gkv1126.
24. Leitner, A., Joachimiak, L.A., Bracher, A., Mönkemeyer, L., Walzthoeni, T., Chen, B., et al. The molecular architecture of the eukaryotic chaperonin TRiC/CCT. Structure (London, England: 1993) 20:5 (2012), 814–825.
25. Ludtke, S.J., Baldwin, P.R., Chiu, W., EMAN: Semiautomated software for high-resolution single-particle reconstructions. Journal of Structural Biology 128:1 (1999), 82–97.
26. Ludtke, S.J., Jakana, J., Song, J.L., Chuang, D.T., Chiu, W., A 11.5 Å single particle reconstruction of GroEL using EMAN. Journal of Molecular Biology 314:2 (2001), 253–262.
27. Marabini, R., Ludtke, S.J., Murray, S.C., Chiu, W., Jose, M., Patwardhan, A., et al. The electron microscopy exchange (EMX) initiative. Journal of Structural Biology 194 (2016), 156–163.
28. Mindell, J.A., Grigorieff, N., Accurate determination of local defocus and specimen tilt in electron microscopy. Journal of Structural Biology 142:3 (2003), 334–347.
29. 3R1 channel. Structure (London, England: 1993) 21:6 (2013), 900–909.
30. Nguyen, T.H., Galej, W.P., Bai, X.C., Savva, C.G., Newman, A.J., Scheres, S.H., et al. The architecture of the spliceosomal U4/U6.U5 tri-snRNP. Nature 523:7558 (2015), 47–52.
31. Park, E., Ménétret, J.F., Gumbart, J.C., Ludtke, S.J., Li, W., Whynot, A., et al. Structure of the SecY channel during initiation of protein translocation. Nature 506:7486 (2014), 102–106.
32. Penczek, P.A., Yang, C., Frank, J., Spahn, C.M., Estimation of variance in single-particle reconstruction using the bootstrap technique. Journal of Structural Biology 154:2 (2006), 168–183.
33. Rohou, A., Grigorieff, N., CTFFIND4: Fast and accurate defocus estimation from electron micrographs. Journal of Structural Biology 192:2 (2015), 216–221.
34. Roseman, A.M., Chen, S., White, H., Braig, K., Saibil, H.R., The chaperonin ATPase cycle: Mechanism of allosteric switching and movements of substrate-binding domains in GroEL. Cell 87:2 (1996), 241–251.
35. Rosenthal, P.B., Henderson, R., Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology 333:4 (2003), 721–745.
36. Scheres, S.H., RELION: Implementation of a Bayesian approach to cryo-EM structure determination. Journal of Structural Biology 180:3 (2012), 519–530.
37. Schmid, M.F., Booth, C.R., Methods for aligning and for averaging 3D volumes with missing data. Journal of Structural Biology 161:3 (2008), 243–248.
38. Schur, F.K., Hagen, W.J., de Marco, A., Briggs, J.A., Determination of protein structure at 8.5 Å resolution using cryo-electron tomography and sub-tomogram averaging. Journal of Structural Biology 184:3 (2013), 394–400.
39. Shahmoradian, S.H., Galaz-Montoya, J.G., Schmid, M.F., Cong, Y., Ma, B., Spiess, C., et al. TRiC's tricks inhibit huntingtin aggregation. eLife, 2, 2013, e00710.
40. Shaikh, T.R., Gao, H., Baxter, W.T., Asturias, F.J., Boisset, N., Leith, A., et al. SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nature Protocols 3:12 (2008), 1941–1974.
41. Stewart, A., Grigorieff, N., Noise bias in the refinement of structures derived from single particles. Ultramicroscopy 102:1 (2004), 67–84.
42. Tang, G., Peng, L., Baldwin, P.R., Mann, D.S., Jiang, W., Rees, I., et al. EMAN2: An extensible image processing suite for electron microscopy. Journal of Structural Biology 157:1 (2007), 38–46.
43. van Heel, M., Harauz, G., Orlova, E.V., Schmidt, R., Schatz, M., A new generation of the IMAGIC image processing system. Journal of Structural Biology 116:1 (1996), 17–24.
44. Xiang, Y., Morais, M.C., Battisti, A.J., Grimes, S., Jardine, P.J., Anderson, D.L., et al. Structural changes of bacteriophage φ29 upon DNA packaging and release. The EMBO Journal 25:21 (2006), 5229–5239.
45. Zhang, J., Baker, M.L., Schröder, G.F., Douglas, N.R., Reissmann, S., Jakana, J., et al. Mechanism of folding chamber closure in a group II chaperonin. Nature 463:7279 (2010), 379–383.
46. Zhang, W., Kimmel, M., Spahn, C.M., Penczek, P.A., Heterogeneity of large macromolecular complexes revealed by 3D cryo-EM variance analysis. Structure (London, England: 1993) 16:12 (2008), 1770–1776.
47. Zhang, J., Minary, P., Levitt, M., Multiscale natural moves refine macromolecules using single-particle electron microscopy projection images. Proceedings of the National Academy of Sciences of the United States of America 109:25 (2012), 9845–9850.