An Approach for De Novo Structure Determination of Dynamic Molecular Assemblies by Electron Cryomicroscopy

Structure

Volumn 18, Issue 6, 2010, Pages 667-676

  Sander, Bjoern ^a,b   Golas, Monika M ^a,b   Lührmann, Reinhard ^b   Stark, Holger ^b,c  

^a AARHUS UNIVERSITY   (Denmark)

^b MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

^c UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

Proteins; RNA

Indexed keywords

SMALL NUCLEAR RIBONUCLEOPROTEIN; MACROMOLECULE;

ADSORPTION; ARTICLE; CONTROLLED STUDY; CRYOELECTRON MICROSCOPY; ESCHERICHIA COLI; MOLECULAR DYNAMICS; MULTIVARIATE ANALYSIS; PRIORITY JOURNAL; RIBOSOME; SIGNAL NOISE RATIO; STRUCTURE ANALYSIS; ANALYSIS; CHEMISTRY; HUMAN; IMAGE PROCESSING; MACROMOLECULE; PROCEDURES; SPLICEOSOME;

CRYOELECTRON MICROSCOPY; ESCHERICHIA COLI; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MACROMOLECULAR SUBSTANCES; RIBOSOMES; SPLICEOSOMES;

ESCHERICHIA COLI;

EID: 77953565575     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2010.05.001     Document Type: Article

References (43)

1. Adrian M., Dubochet J., Lepault J., McDowall A.W. Cryo-electron microscopy of viruses. Nature 1984, 308:32-36.
2. Alberts B. The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 1998, 92:291-294.
3. Ban N., Nissen P., Hansen J., Moore P.B., Steitz T.A. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 2000, 289:905-920.
4. 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 2004, 12:185-191.
5. Carter A.P., Clemons W.M., Brodersen D.E., Morgan-Warren R.J., Wimberly B.T., Ramakrishnan V. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 2000, 407:340-348.
6. Cheng Y., Wolf E., Larvie M., Zak O., Aisen P., Grigorieff N., Harrison S.C., Walz T. Single particle reconstructions of the transferrin-transferrin receptor complex obtained with different specimen preparation techniques. J. Mol. Biol. 2006, 355:1048-1065.
7. Crowther R.A. Procedures for three-dimensional reconstruction of spherical viruses by Fourier synthesis from electron micrographs. Philos. Trans. R. Soc. Lond. B Biol. Sci. 1971, 261:221-230.
8. Diaconu M., Kothe U., Schlünzen F., Fischer N., Harms J.M., Tonevitsky A.G., Stark H., Rodnina M.V., Wahl M.C. Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation. Cell 2005, 121:991-1004.
9. Frank J., Al-Ali L. Signal-to-noise ratio of electron micrographs obtained by cross correlation. Nature 1975, 256:376-379.
10. Gavin A., Bösche M., Krause R., Grandi P., Marzioch M., Bauer A., Schultz J., Rick J.M., Michon A., Cruciat C., et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415:141-147.
11. Golas M.M., Böhm C., Sander B., Effenberger K., Brecht M., Stark H., Göringer H.U. Snapshots of the RNA editing machine in trypanosomes captured at different assembly stages in vivo. EMBO J. 2009, 28:766-778.
12. Grob P., Cruse M.J., Inouye C., Peris M., Penczek P.A., Tjian R., Nogales E. Cryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues. Structure 2006, 14:511-520.
13. Hall R.J., Siridechadilok B., Nogales E. Cross-correlation of common lines: a novel approach for single-particle reconstruction of a structure containing a flexible domain. J. Struct. Biol. 2007, 159:474-482.
14. Joyeux L., Penczek P.A. Efficiency of 2D alignment methods. Ultramicroscopy 2002, 92:33-46.
15. Leschziner A.E., Nogales E. The orthogonal tilt reconstruction method: an approach to generating single-class volumes with no missing cone for ab initio reconstruction of asymmetric particles. J. Struct. Biol. 2006, 153:284-299.
16. Leschziner A.E., Nogales E. Visualizing flexibility at molecular resolution: analysis of heterogeneity in single-particle electron microscopy reconstructions. Annu. Rev. Biophys. Biomol. Struct. 2007, 36:43-62.
17. Liu J., Reedy M.C., Goldman Y.E., Franzini-Armstrong C., Sasaki H., Tregear R.T., Lucaveche C., Winkler H., Baumann B.A.J., Squire J.M., et al. Electron tomography of fast frozen, stretched rigor fibers reveals elastic distortions in the myosin crossbridges. J. Struct. Biol. 2004, 147:268-282.
18. Lucić V., Förster F., Baumeister W. Structural studies by electron tomography: from cells to molecules. Annu. Rev. Biochem. 2005, 74:833-865.
19. McMullan G., Faruqi A.R., Henderson R., Guerrini N., Turchetta R., Jacobs A., van Hoften G. Experimental observation of the improvement in MTF from backthinning a CMOS direct electron detector. Ultramicroscopy 2009, 109:1144-1147.
20. Mitra K., Frank J. Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps. Annu. Rev. Biophys. Biomol. Struct. 2006, 35:299-317.
21. Nickell S., Kofler C., Leis A.P., Baumeister W. A visual approach to proteomics. Nat. Rev. Mol. Cell Biol. 2006, 7:225-230.
22. Oeffinger M., Wei K.E., Rogers R., DeGrasse J.A., Chait B.T., Aitchison J.D., Rout M.P. Comprehensive analysis of diverse ribonucleoprotein complexes. Nat. Methods 2007, 4:951-956.
23. Penczek P.A., Grassucci R.A., Frank J. The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles. Ultramicroscopy 1994, 53:251-270.
24. Penczek P.A., Frank J., Spahn C.M.T. A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation. J. Struct. Biol. 2006, 154:184-194.
25. Radermacher M., Wagenknecht T., Verschoor A., Frank J. Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli. J. Microsc. 1987, 146:113-136.
26. Rosenthal P.B., Henderson R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 2003, 333:721-745.
27. Rubinstein J.L., Walker J.E., Henderson R. Structure of the mitochondrial ATP synthase by electron cryomicroscopy. EMBO J. 2003, 22:6182-6192.
28. Sander B., Golas M.M., Stark H. Automatic CTF correction for single particles based upon multivariate statistical analysis of individual power spectra. J. Struct. Biol. 2003, 142:392-401.
29. Sander B., Golas M.M., Stark H. Corrim-based alignment for improved speed in single-particle image processing. J. Struct. Biol. 2003, 143:219-228.
30. Sander B., Golas M.M., Makarov E.M., Brahms H., Kastner B., Lührmann R., Stark H. Organization of core spliceosomal components U5 snRNA loop I and U4/U6 di-snRNP within U4/U6.U5 tri-snRNP as revealed by electron cryomicroscopy. Mol. Cell 2006, 24:267-278.
31. Scheres S.H.W., Gao H., Valle M., Herman G.T., Eggermont P.P.B., Frank J., Carazo J. Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. Nat. Methods 2007, 4:27-29.
32. Scheres S.H.W., Melero R., Valle M., Carazo J. Averaging of electron subtomograms and random conical tilt reconstructions through likelihood optimization. Structure 2009, 17:1563-1572.
33. Scheres S.H.W., Valle M., Grob P., Nogales E., Carazo J. Maximum likelihood refinement of electron microscopy data with normalization errors. J. Struct. Biol. 2009, 166:234-240.
34. Schmid M.F., Booth C.R. Methods for aligning and for averaging 3D volumes with missing data. J. Struct. Biol. 2008, 161:243-248.
35. Schuwirth B.S., Borovinskaya M.A., Hau C.W., Zhang W., Vila-Sanjurjo A., Holton J.M., Cate J.H.D. Structures of the bacterial ribosome at 3.5 Å resolution. Science 2005, 310:827-834.
36. Sigworth F.J. A maximum-likelihood approach to single-particle image refinement. J. Struct. Biol. 1998, 122:328-339.
37. Simonetti A., Marzi S., Myasnikov A.G., Fabbretti A., Yusupov M., Gualerzi C.O., Klaholz B.P. Structure of the 30S translation initiation complex. Nature 2008, 455:416-420.
38. Sousa D., Grigorieff N. Ab initio resolution measurement for single particle structures. J. Struct. Biol. 2007, 157:201-210.
39. van Heel M. Multivariate statistical classification of noisy images (randomly oriented biological macromolecules). Ultramicroscopy 1984, 13:165-183.
40. van Heel M. Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy 1987, 21:111-123.
41. van Heel M., Harauz G., Orlova E.V., Schmidt R., Schatz M. A new generation of the IMAGIC image processing system. J. Struct. Biol. 1996, 116:17-24.
42. Wahl M.C., Will C.L., Lührmann R. The spliceosome: design principles of a dynamic RNP machine. Cell 2009, 136:701-718.
43. Zemlin F. Dynamic focussing for recording images from tilted samples in small-spot scanning with a transmission electron microscope. J. Electron Microsc. Tech. 1989, 11:251-257.