Heterogeneity of Large Macromolecular Complexes Revealed by 3D Cryo-EM Variance Analysis

Structure

Volumn 16, Issue 12, 2008, Pages 1770-1776

  Zhang, Wei ^a   Kimmel, Marek ^b   Spahn, Christian M T ^c   Penczek, Pawel A ^a  

^a UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

^b Rice University   (United States)

^c CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

Author keywords

PROTEINS

Indexed keywords

ELONGATION FACTOR G; TRANSFER RNA;

ALGORITHM; ANALYSIS OF VARIANCE; ARTICLE; BOOTSTRAPPING; CHEMICAL STRUCTURE; CONFORMATION; CONFORMATIONAL TRANSITION; CRYOELECTRON MICROSCOPY; FOURIER TRANSFORMATION; MACROMOLECULE; OPTICAL RESOLUTION; PRIORITY JOURNAL; RIBOSOME; VALIDATION PROCESS;

ALGORITHMS; ANALYSIS OF VARIANCE; COMPUTER SIMULATION; CRYOELECTRON MICROSCOPY; IMAGING, THREE-DIMENSIONAL; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PEPTIDE ELONGATION FACTOR G; REPRODUCIBILITY OF RESULTS; RIBOSOMES; RNA, BACTERIAL; RNA, TRANSFER; THERMUS THERMOPHILUS;

EID: 57049145347     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2008.10.011     Document Type: Article

References (32)

1. Allen G.S., Zavialov A., Gursky R., Ehrenberg M., and Frank J. The cryo-EM structure of a translation initiation complex from Escherichia coli. Cell 121 (2005) 703-712
2. Bracewell R.N. Strip integration in radio astronomy. Aust. J. Phys. 9 (1956) 198-217
3. Bracewell R.N., and Riddle A.C. Inversion of fan-beam scans in radio astronomy. Astrophys. J. 150 (1967) 427-434
4. Connell S.R., Takemoto C., Wilson D.N., Wang H., Murayama K., Terada T., Shirouzu M., Rost M., Schuler M., Giesebrecht J., et al. Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. Mol. Cell 25 (2007) 751-764
5. Davison A.C., and Hinkley D.V. Bootstrap methods and their application (1997), Cambridge University Press, New York
6. Frank J., and Agrawal R.K. A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature 406 (2000) 318-322
7. Frank J., Verschoor A., and Boublik M. Computer averaging of electron micrographs of 40S ribosomal subunits. Science 214 (1981) 1353-1355
8. Gao H., Zhou Z., Rawat U., Huang C., Bouakaz L., Wang C., Cheng Z., Liu Y., Zavialov A., Gursky R., et al. RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors. Cell 129 (2007) 929-941
9. Gilbert R.J.C., Gordiyenko Y., von der Haar T., Sonnen A.F.-P., Hofmann G., Nardelli M., Stuart D.I., and McCarthy J.E.G. Reconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex. Proc. Natl. Acad. Sci. USA 104 (2007) 5788-5793
10. Grob P., Cruse M.J., Inouye C., Peris M., Penczek P.A., Tjian R., and Nogales E. Cryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues. Structure 14 (2006) 511-520
11. Hansen M.H., Hurwitz W.N., and Madow W.G. Sample survey methods and theory Volume 2 (1953), Wiley, New York
12. Harauz G., and van Heel M. Exact filters for general geometry three dimensional reconstruction. Optik 73 (1986) 146-156
13. Hohn M., Tang G., Goodyear G., Baldwin P.R., Huang Z., Penczek P.A., Yang C., Glaeser R.M., Adams P.D., and Ludtke S.J. SPARX, a new environment for Cryo-EM image processing. J. Struct. Biol. 157 (2007) 47-55
14. Ludtke S.J., Baker M.L., Chen D.H., Song J.L., Chuang D.T., and Chiu W. De novo backbone trace of GroEL from single particle electron cryomicroscopy. Structure 16 (2008) 441-448
15. Ohi M.D., Feoktistova A., Ren L.P., Yip C., Cheng Y.F., Chen J.S., Yoon H.J., Wall J.S., Huang Z., Penczek P.A., et al. Structural organization of the anaphase-promoting complex bound to the mitotic activator Slp1. Mol. Cell 28 (2007) 871-885
16. Penczek P., Radermacher M., and Frank J. Three-dimensional reconstruction of single particles embedded in ice. Ultramicroscopy 40 (1992) 33-53
17. Penczek P.A. Three-dimensional spectral signal-to-noise ratio for a class of reconstruction algorithms. J. Struct. Biol. 138 (2002) 34-46
18. Penczek P.A., Chao Y., Frank J., and Spahn C.M.T. Estimation of variance in single particle reconstruction using the bootstrap technique. J. Struct. Biol. 154 (2006) 168-183
19. Penczek P.A., Grassucci R.A., and Frank J. The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles. Ultramicroscopy 53 (1994) 251-270
20. Penczek P.A., Zhu J., Schröder R., and Frank J. Three-dimensional reconstruction with contrast transfer function compensation from defocus series. Scanning Microsc. Suppl. 11 (1997) 147-154
21. Penczek P.A., Renka R., and Schomberg H. Gridding-based direct Fourier inversion of the three-dimensional ray transform. J. Opt. Soc. Am. A Opt. Image Sci. Vis. 21 (2004) 499-509
22. Radermacher M. Weighted back-projection methods. In: Frank J. (Ed). Electron Tomography (1992), Plenum, New York 91-115
23. Rivera-Calzada A., Spagnolo L., Pearl L.H., and Llorca O. Structural model of full-length human Ku70-Ku80 heterodimer and its recognition of DNA and DNA-PKcs. EMBO Rep. 8 (2007) 56-62
24. Saxton W.O., and Baumeister W. The correlation averaging of a regularly arranged bacterial envelope protein. J. Microsc. 127 (1982) 127-138
25. Schüler M., Connell S.R., Lescoute A., Giesebrecht J., Dabrowski M., Schroeer B., Mielke T., Penczek P.A., Westhof E., and Spahn C.M.T. Structure of the ribosome-bound cricket paralysis virus IRES RNA. Nat. Struct. Mol. Biol. 13 (2006) 1092-1096
26. Schuwirth B.S., Borovinskaya M.A., Hau C.W., Zhang W., Vila-Sanjurjo A., Holton J.M., and Cate J.H. Structures of the bacterial ribosome at 3.5 A resolution. Science 310 (2005) 827-834
27. Selmer M., Dunham C.M., Murphy F.V., Weixlbaumer A., Petry S., Kelley A.C., Weir J.R., and Ramakrishnan V. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313 (2006) 1935-1942
28. Spahn C.M., Gomez-Lorenzo M.G., Grassucci R., Jorgensen R., Andersen G.R., Beckmann R., Penczek P.A., Ballesta J.P., and Frank J. Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. EMBO J. 23 (2004) 1008-1019
29. Spahn C.M.T., Blaha G., Agrawal R.K., Penczek P., Grassucci R.A., Trieber C.A., Connell S.R., Taylor D.E., Nierhaus K.H., and Frank J. Localization of the ribosomal protection protein Tet(O) on the ribosome and the mechanism of tetracycline resistance. Mol. Cell 7 (2001) 1037-1045
30. Unser M., Trus B.L., and Steven A.C. A new resolution criterion based on spectral signal-to-noise ratios. Ultramicroscopy 23 (1987) 39-51
31. Valle M., Zavialov A., Sengupta J., Rawat U., Ehrenberg M., and Frank J. Locking and unlocking of ribosomal motions. Cell 114 (2003) 123-134
32. van Heel M., Gowen B., Matadeen R., Orlova E.V., Finn R., Pape T., Cohen D., Stark H., Schmidt R., Schatz M., and Patwardhan A. Single-particle electron cryo-microscopy: towards atomic resolution. Q. Rev. Biophys. 33 (2000) 307-369