Single-particle applications at intermediate resolution

Advances in Protein Chemistry and Structural Biology

Volumn 81, Issue C, 2010, Pages 61-88

  Böttcher, Bettina ^a   Hipp, Katharina ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 78649649421     PISSN: 18761623     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-381357-2.00003-7     Document Type: Chapter

References (70)

1. P. Aloy, B. Bottcher, H. Ceulemans, C. Leutwein, C. Mellwig, and S. Fischer Structure-based assembly of protein complexes in yeast Science 303 2004 2026 2029
2. P. Aloy, F.D. Ciccarelli, C. Leutwein, A.C. Gavin, G. Superti-Furga, and P. Bork A complex prediction: three-dimensional model of the yeast exosome EMBO Rep. 3 2002 628 635
3. M. Beck, J.A. Malmstrom, V. Lange, A. Schmidt, E.W. Deutsch, and R. Aebersold Visual proteomics of the human pathogen Leptospira interrogans Nat. Methods 6 2009 817 823
4. J. Berriman, and K.R. Leonard Methods for specimen thickness determination in electron microscopy. II. Changes in thickness with dose Ultramicroscopy 19 1986 349 366
5. J. Bhm, A.S. Frangakis, R. Hegerl, S. Nickell, D. Typke, and W. Baumeister From the cover: toward detecting and identifying macromolecules in a cellular context: template matching applied to electron tomograms Proc. Natl. Acad. Sci. USA 97 2000 14245 14250
6. B. Bttcher, M. Vogel, M. Ploss, and M. Nassal High plasticity of the hepatitis B virus capsid revealed by conformational stress J. Mol. Biol. 356 2006 812 822
7. S. Brenner, and R.W. Horne A negative staining method for high resolution electron microscopy of viruses Biochim. Biophys. Acta 34 1959 103 110
8. H. Ceulemans, and R.B. Russell Fast fitting of atomic structures to low-resolution electron density maps by surface overlap maximization J. Mol. Biol. 338 2004 783 793
9. A. Charpilienne, M. Nejmeddine, M. Berois, N. Parez, E. Neumann, and E. Hewat Individual rotavirus-like particles containing 120 molecules of fluorescent protein are visible in living cells J. Biol. Chem. 276 2001 29361 29367
10. Z.A. Chen, A. Jawhari, L. Fischer, C. Buchen, S. Tahir, and T. Kamenski Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry EMBO J. 29 2010 717 726
11. N. Cheng, J.F. Conway, N.R. Watts, J.F. Hainfeld, V. Joshi, and R.D. Powell Tetrairidium, a four-atom cluster, is readily visible as a density label in three-dimensional cryo-EM maps of proteins at 10-25 A resolution J. Struct. Biol. 127 1999 169 176
12. J.F. Conway, S.K. Cockrell, A.M. Copeland, W.W. Newcomb, J.C. Brown, and F.L. Homa Labeling and localization of the herpes simplex virus capsid protein UL25 and its interaction with the two triplexes closest to the penton J. Mol. Biol. 397 2010 575 586
13. R.A. Crowther, D.J. DeRosier, and A. Klug The reconstruction of a three-dimensional structure from projections and its application to electron microscopy Proc. R. Soc Lond. A A317 1970 319 340
14. D.J. DeRosier, and A. Klug Reconstruction of three dimensinal structures from electron micrographes Nature 217 1968 130 134
15. E. Di Luccio, B. Petschacher, J. Voegtli, H.T. Chou, H. Stahlberg, and B. Nidetzky Structural and kinetic studies of induced fit in xylulose kinase from Escherichia coli J. Mol. Biol. 365 2007 783 798
16. M. Diepholz, D. Venzke, S. Prinz, C. Batisse, B. Florchinger, and M. Rossle A different conformation for EGC stator subcomplex in solution and in the assembled yeast V-ATPase: possible implications for regulatory disassembly Structure 16 2008 1789 1798
17. J. Dubochet, M. Adrian, J.J. Chang, J.C. Homo, J. Lepault, and A.W. McDowall Cryo-electron microscopy of vitrified specimens Q. Rev. Biophys. 21 1988 129 228
18. N. Fischer, A.L. Konevega, W. Wintermeyer, M.V. Rodnina, and H. Stark Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy Nature 466 2010 329 333
19. D. Flemming, K. Thierbach, P. Stelter, B. Bottcher, and E. Hurt Precise mapping of subunits in multiprotein complexes by a versatile electron microscopy label Nat. Struct. Mol. Biol. 17 2010 775 778
20. A.C. Gavin, M. Bosche, R. Krause, P. Grandi, M. Marzioch, and A. Bauer Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 415 2002 141 147
21. M.M. Golas, B. Sander, C.L. Will, R. Luhrmann, and H. Stark Molecular architecture of the multiprotein splicing factor SF3b Science 300 2003 980 984
22. J.F. Hainfeld Labeling with nanogold and undecagold: techniques and results Scanning Microsc. Suppl. 10 1996 309 322
23. J.F. Hainfeld, D. Safer, J.S. Wall, M. Simon, B. Lin, and R.D. Powell Methylamine vanadate (NanoVan) negative stain G.W. Bailey, A.J. Garratt-Reed, Proc. 52nd Ann. Mtg. Micros. Soc. Amer. 1994 San Francisco Press San Francisco 132 133
24. B.G. Han, M. Dong, H. Liu, L. Camp, J. Geller, and M. Singer Survey of large protein complexes in D. vulgaris reveals great structural diversity Proc. Natl. Acad. Sci. USA 106 2009 16580 16585
25. C.M. John, R.K. Hite, C.S. Weirich, D.J. Fitzgerald, H. Jawhari, and M. Faty The Caenorhabditis elegans septin complex is nonpolar EMBO J. 26 2007 3296 3307
26. B. Kastner, N. Fischer, M.M. Golas, B. Sander, P. Dube, and D. Boehringer GraFix: sample preparation for single-particle electron cryomicroscopy Nat. Methods 5 2008 53 55
27. T. Kato, H. Yoshida, T. Miyata, Y. Maki, A. Wada, and K. Namba Structure of the 100 S ribosome in the hibernation stage revealed by electron cryomicroscopy Structure 18 2010 719 724
28. D.F. Kelly, P.D. Abeyrathne, D. Dukovski, and T. Walz The Affinity Grid: a pre-fabricated EM grid for monolayer purification J. Mol. Biol. 382 2008 423 433
29. S. Kronenberg, J.A. Kleinschmidt, and B. Bottcher Electron cryo-microscopy and image reconstruction of adeno-associated virus type 2 empty capsids EMBO Rep. 2 2001 997 1002
30. W. Kuhlbrandt Discrimination of protein and nucleic acids by electron microscopy using contrast variation Ultramicroscopy 7 1982 221 232
31. S. Kuhner, V. van Noort, M.J. Betts, A. Leo-Macias, C. Batisse, and M. Rode Proteome organization in a genome-reduced bacterium Science 326 2009 1235 1240
32. J.A. Lake, M. Pendergast, L. Kahan, and M. Nomura Ribosome structure: three-dimensional distribution of proteins S14 and S4 J. Supramol. Struct. 2 1974 189 195
33. A.E. Leschziner, and E. Nogales 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. 153 2006 284 299
34. D.N. Mastronarde Automated electron microscope tomography using robust prediction of specimen movements J. Struct. Biol. 152 2005 36 51
35. C.P. Mercogliano, and D.J. DeRosier Concatenated metallothionein as a clonable gold label for electron microscopy J. Struct. Biol. 160 2007 70 82
36. R.A. Milligan, and D. Safer Molecular structure of F-actin and location of surface binding sites Nature 348 1990 217 221
37. S.P. Muench, M. Huss, C.F. Song, C. Phillips, H. Wieczorek, and J. Trinick Cryo-electron microscopy of the vacuolar ATPase motor reveals its mechanical and regulatory complexity J. Mol. Biol. 386 2009 989 999
38. J.B. Munro, K.Y. Sanbonmatsu, C.M. Spahn, and S.C. Blanchard Navigating the ribosome's metastable energy landscape Trends Biochem. Sci. 34 2009 390 400
39. N.H. Olson, P.R. Kolatkar, M.A. Oliveria, R.H. Cheng, J.M. Greve, and A. McClelland Structure of human rhinovirus complexed with its receptor molecule Proc. Natl. Acad. Sci. 90 1993 507 511
40. E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, and E.C. Meng UCSF Chimeraa visualization system for exploratory research and analysis J. Comput. Chem. 25 2004 1605 1612
41. O. Puig, F. Caspary, G. Rigaut, B. Rutz, E. Bouveret, and E. Bragado-Nilsson The tandem affinity purification (TAP) method: a general procedure of protein complex purification Methods 24 2001 218 229
42. M. Radermacher Three-dimensional reconstruction of single particles from random and nonrandom tilt series J. Electron Microsc. Tech. 9 1988 359 394
43. A.J. Roberts, N. Numata, M.L. Walker, Y.S. Kato, B. Malkova, and T. Kon AAA+ Ring and linker swing mechanism in the dynein motor Cell 136 2009 485 495
44. M. Sagermann, T.H. Stevens, and B.W. Matthews Crystal structure of the regulatory subunit H of the V-type ATPase of Saccharomyces cerevisiae Proc. Natl. Acad. Sci. USA 98 2001 7134 7139
45. B. Sander, M.M. Golas, R. Luhrmann, and H. Stark An approach for de novo structure determination of dynamic molecular assemblies by electron cryomicroscopy Structure 18 2010 667 676
46. B. Sander, M.M. Golas, and H. Stark Advantages of CCD detectors for de novo three-dimensional structure determination in single-particle electron microscopy J. Struct. Biol. 151 2005 92 105
47. S.H. Scheres, R. Nunez-Ramirez, Y. Gomez-Llorente, C. San Martin, P.P. Eggermont, and J.M. Carazo Modeling experimental image formation for likelihood-based classification of electron microscopy data Structure 15 2007 1167 1177
48. H. Stark, P. Dube, R. Luhrmann, and B. Kastner Arrangement of RNA and proteins in the spliceosomal U1 small nuclear ribonucleoprotein particle Nature 409 2001 539 542
49. P.L. Stewart, S.D. Fuller, and R.M. Burnett Difference imaging of adenovirus; bridging the resolution gap between X-ray crystallography and electron microscopy EMBO J. 12 1993 2589 2599
50. M.E. Stroupe, C. Xu, B.L. Goode, and N. Grigorieff Actin filament labels for localizing protein components in large complexes viewed by electron microscopy RNA 15 2009 244 248
51. K. Suhre, J. Navaza, and Y.H. Sanejouand NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps Acta Crystallogr. D Biol. Crystallogr. 62 2006 1098 1100
52. C. Suloway, J. Pulokas, D. Fellmann, A. Cheng, F. Guerra, and J. Quispe Automated molecular microscopy: the new Leginon system J. Struct. Biol. 151 2005 41 60
53. F. Tama, O. Miyashita, and C.L. Brooks III Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis J. Mol. Biol. 337 2004 985 999
54. B.L. Trus, R.B. Roden, H.L. Greenstone, M. Vrhel, J.T. Schiller, and F.P. Booy Novel structural features of bovine papillomavirus capsid revealed by a three-dimensional reconstruction to 9 A resolution Nat. Struct. Biol. 4 1997 413 420
55. C. Ulbrich, M. Diepholz, J. Bassler, D. Kressler, B. Pertschy, and K. Galani Mechanochemical removal of ribosome biogenesis factors from nascent 60 S ribosomal subunits Cell 138 2009 911 922
56. P.N.T. Unwin Electron-microscopy of stacked disk aggregate of tobacco mosaic-virus protein. 2. Influence of electron-irradiation on stain distribution J. Mol. Biol. 87 1974 657 664
57. M. van Heel Multivariate statistical classification of noisy images (randomly oriented biological macromolecules) Ultramicroscopy 13 1984 165 183
58. M. van Heel Angular reconstruction: a posteriori assignment of projection directions from 3D reconstruction Ultramicroscopy 21 1987 111 124
59. M. van Heel, and J. Frank Use of multivariate statistics in analysing the images of biological macromolecules Ultramicroscopy 6 1981 187 194
60. N.R. Voss, D. Lyumkis, A. Cheng, P.W. Lau, A. Mulder, and G.C. Lander A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy J. Struct. Biol. 169 2010 389 398
61. R.H. Wade A brief look at imaging and contrast transfer Ultramicroscopy 46 1992 145 156
62. G.J. Wang, C. Porta, Z.G. Chen, T.S. Baker, and J.E. Johnson Identification of a Fab interaction footprint site on an icosahedral virus by cryoelectron microscopy and X-ray crystallography Nature 355 1992 275 278
63. S. Wilkens, and R.A. Capaldi Monomaleimidogold labeling of the gamma subunit of the Escherichia coli F1 ATPase examined by cryoelectron microscopy Arch. Biochem. Biophys. 299 1992 105 109
64. E. Wolf, B. Kastner, J. Deckert, C. Merz, H. Stark, and R. Luhrmann Exon, intron and splice site locations in the spliceosomal B complex EMBO J. 28 2009 2283 2292
65. W. Wriggers, and S. Birmanns Using situs for flexible and rigid-body fitting of multiresolution single-molecule data J. Struct. Biol. 133 2001 193 202
66. C. Yoshioka, J. Pulokas, D. Fellmann, C.S. Potter, R.A. Milligan, and B. Carragher Automation of random conical tilt and orthogonal tilt data collection using feature-based correlation J. Struct. Biol. 159 2007 335 346
67. X. Yu, L. Jin, and Z.H. Zhou 3.88 A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy Nature 453 2008 415 419
68. X. Zhang, E. Settembre, C. Xu, P.R. Dormitzer, R. Bellamy, and S.C. Harrison Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction Proc. Natl. Acad. Sci. USA 105 2008 1867 1872
69. Z. Zhang, Y. Zheng, H. Mazon, E. Milgrom, N. Kitagawa, and E. Kish-Trier Structure of the yeast vacuolar ATPase J. Biol. Chem. 283 2008 35983 35995
70. A. Zlotnick, N. Cheng, S.J. Stahl, J.F. Conway, A.C. Steven, and P.T. Wingfield Localization of the C terminus of the assembly domain of hepatitis B virus capsid protein: implications for morphogenesis and organization of encapsidated RNA Proc. Natl. Acad. Sci. USA 94 1997 9556 9561