Electron cryomicroscopy of single particles at subnanometer resolution

Current Opinion in Structural Biology

Volumn 15, Issue 5, 2005, Pages 571-577

  Jiang, Wen ^a   Ludtke, Steven J ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLATHRIN; RYANODINE RECEPTOR; VIRUS PROTEIN;

ALPHA HELIX; BETA SHEET; CRYOELECTRON MICROSCOPY; CRYSTAL STRUCTURE; DNA VIRUS; HUMAN; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN FOLDING; PROTEIN STRUCTURE; REVIEW; RIBOSOME; RNA VIRUS; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

ANIMALS; CLATHRIN; CRYOELECTRON MICROSCOPY; GROEL PROTEIN; HUMANS; MODELS, MOLECULAR; NANOSTRUCTURES; RIBOSOMES; RYANODINE RECEPTOR CALCIUM RELEASE CHANNEL; VIRAL PROTEINS; VIRUSES;

EID: 25844445494     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2005.08.004     Document Type: Review

References (44)

1. B. Bottcher, S.A. Wynne, and R.A. Crowther Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy Nature 386 1997 88 91
2. J.F. Conway, N. Cheng, A. Zlotnick, P.T. Wingfield, S.J. Stahl, and A.C. Steven Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy Nature 386 1997 91 94
3. C. Xiao, T.J. Tuthill, C.M. Bator Kelly, L.J. Challinor, P.R. Chipman, R.A. Killington, D.J. Rowlands, A. Craig, and M.G. Rossmann Discrimination among rhinovirus serotypes for a variant ICAM-1 receptor molecule J Virol 78 2004 10034 10044 The structures of several variants of rhinoviruses and their cellular receptors were determined to around 10 Å resolution using cryo-EM. By fitting the crystal structures of both virus capsid and the receptor, detailed analysis of the binding sites was performed, revealing the mechanisms of differential binding characteristics.
4. S.D. Saban, R.R. Nepomuceno, L.D. Gritton, G.R. Nemerow, and P.L. Stewart CryoEM structure at 9 Å resolution of an adenovirus vector targeted to hematopoietic cells J Mol Biol 349 2005 526 537
5. C.M. Fabry, M. Rosa-Calatrava, J.F. Conway, C. Zubieta, S. Cusack, R.W. Ruigrok, and G. Schoehn A quasi-atomic model of human adenovirus type 5 capsid EMBO J 24 2005 1645 1654
6. Z.H. Zhou, M. Dougherty, J. Jakana, J. He, F.J. Rixon, and W. Chiu Seeing the herpesvirus capsid at 8.5 Å Science 288 2000 877 880
7. Z.H. Zhou, H. Zhang, J. Jakana, X.Y. Lu, and J.Q. Zhang Cytoplasmic polyhedrosis virus structure at 8 Å by electron cryomicroscopy: structural basis of capsid stability and mRNA processing regulation Structure 11 2003 651 663
8. Z.H. Zhou, M.L. Baker, W. Jiang, M. Dougherty, J. Jakana, G. Dong, G. Lu, and W. Chiu Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus Nat Struct Biol 8 2001 868 873
9. X. Zhang, S.B. Walker, P.R. Chipman, M.L. Nibert, and T.S. Baker Reovirus polymerase lambda 3 localized by cryo-electron microscopy of virions at a resolution of 7.6 Å Nat Struct Biol 10 2003 1011 1018 Icosahedral reconstruction of the reovirus structure was mined to localize the embedded polymerase by fitting the crystal structures of all components. This is an example of deriving non-icosahedral component information for an icosahedral virus.
10. E.J. Mancini, M. Clarke, B.E. Gowen, T. Rutten, and S.D. Fuller Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus Mol Cell 5 2000 255 266
11. W. Zhang, P.R. Chipman, J. Corver, P.R. Johnson, Y. Zhang, S. Mukhopadhyay, T.S. Baker, J.H. Strauss, M.G. Rossmann, and R.J. Kuhn Visualization of membrane protein domains by cryo-electron microscopy of dengue virus Nat Struct Biol 10 2003 907 912
12. J.T. Huiskonen, H.M. Kivela, D.H. Bamford, and S.J. Butcher The PM2 virion has a novel organization with an internal membrane and pentameric receptor binding spikes Nat Struct Mol Biol 11 2004 850 856
13. W. Jiang, Z. Li, Z. Zhang, M.L. Baker, P.E. Prevelige Jr., and W. Chiu Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions Nat Struct Biol 10 2003 131 135 Structures of phage P22 at the procapsid and mature phage stages were determined to subnanometer resolutions. This revealed, for the first time, the structural conservation of the major capsid protein fold among tailed dsDNA phages. Procapsid to mature phage maturation is now illustrated at the level of secondary structure element changes.
14. M.C. Morais, K.H. Choi, J.S. Koti, P.R. Chipman, D.L. Anderson, and M.G. Rossmann Conservation of the capsid structure in tailed dsDNA bacteriophages: the pseudoatomic structure of phi29 Mol Cell 18 2005 149 159 The phage φ29 capsid structure was solved at 7.9 Å resolution. The major capsid protein was found to share a similar fold to phage HK97.
15. S.A. Wynne, R.A. Crowther, and A.G. Leslie The crystal structure of the human hepatitis B virus capsid Mol Cell 3 1999 771 780
16. B.R. Bowman, M.L. Baker, F.J. Rixon, W. Chiu, and F.A. Quiocho Structure of the herpesvirus major capsid protein EMBO J 22 2003 757 765 The crystal structure of the upper domain of VP5 from herpes simplex virus validated the earlier cryo-EM structure of the capsid and the assignment of helices.
17. A. Nakagawa, N. Miyazaki, J. Taka, H. Naitow, A. Ogawa, Z. Fujimoto, H. Mizuno, T. Higashi, Y. Watanabe, and T. Omura The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins Structure 11 2003 1227 1238
18. A. Fokine, P.G. Leiman, M.M. Shneider, B. Ahvazi, K.M. Boeshans, A.C. Steven, L.W. Black, V.V. Mesyanzhinov, and M.G. Rossmann Structural and functional similarities between the capsid proteins of bacteriophages T4 and HK97 point to a common ancestry Proc Natl Acad Sci USA 102 2005 7163 7168
19. M.S. Chapman, and L. Liljas Structural folds of viral proteins Adv Protein Chem 64 2003 125 196
20. S.D. Benson, J.K. Bamford, D.H. Bamford, and R.M. Burnett Does common architecture reveal a viral lineage spanning all three domains of life? Mol Cell 16 2004 673 685
21. K.M. Reinisch, M.L. Nibert, and S.C. Harrison Structure of the reovirus core at 3.6 Å resolution Nature 404 2000 960 967
22. J.M. Grimes, J.N. Burroughs, P. Gouet, J.M. Diprose, R. Malby, S. Zientara, P.P. Mertens, and D.I. Stuart The atomic structure of the bluetongue virus core Nature 395 1998 470 478
23. H. Naitow, J. Tang, M. Canady, R.B. Wickner, and J.E. Johnson L-A virus at 3.4 Å resolution reveals particle architecture and mRNA decapping mechanism Nat Struct Biol 9 2002 725 728
24. J.B. Heymann, N. Cheng, W.W. Newcomb, B.L. Trus, J.C. Brown, and A.C. Steven Dynamics of herpes simplex virus capsid maturation visualized by time-lapse cryo-electron microscopy Nat Struct Biol 10 2003 334 341
25. R. Lata, J.F. Conway, N. Cheng, R.L. Duda, R.W. Hendrix, W.R. Wikoff, J.E. Johnson, H. Tsuruta, and A.C. Steven Maturation dynamics of a viral capsid: visualization of transitional intermediate states Cell 100 2000 253 263
26. P.B. Rosenthal, and R. Henderson Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy J Mol Biol 333 2003 721 745
27. M.J. Borgnia, D. Shi, P. Zhang, and J.L. Milne Visualization of alpha-helical features in a density map constructed using 9 molecular images of the 1.8 MDa icosahedral core of pyruvate dehydrogenase J Struct Biol 147 2004 136 145
28. A. Fotin, Y. Cheng, P. Sliz, N. Grigorieff, S.C. Harrison, T. Kirchhausen, and T. Walz Molecular model for a complete clathrin lattice from electron cryomicroscopy Nature 432 2004 573 579 An exceptional example of how subnanometer resolution structures should be presented. α Helices are clearly observed and larger motifs are identified.
29. N.A. Ranson, G.W. Farr, A.M. Roseman, B. Gowen, W.A. Fenton, A.L. Horwich, and H.R. Saibil ATP-bound states of GroEL captured by cryo-electron microscopy Cell 107 2001 869 879
30. S.J. Ludtke, D.H. Chen, J.L. Song, D.T. Chuang, and W. Chiu Seeing GroEL at 6 Å resolution by single particle electron cryomicroscopy Structure 12 2004 1129 1136 The highest resolution single-particle reconstruction to date. This structure also demonstrates measurable differences between the crystal structure and the single-particle reconstruction.
31. E.V. Orlova, B. Gowen, A. Droge, A. Stiege, F. Weise, R. Lurz, M. van Heel, and P. Tavares Structure of a viral DNA gatekeeper at 10 Å resolution by cryo-electron microscopy EMBO J 22 2003 1255 1262 SPP1 phage connector structures were solved in isolation and in complex with head completion proteins. Different symmetries were observed in the two structures. The protein fold was also found to be similar to that of the φ29 phage connector crystal structure.
32. X. Agirrezabala, J. Martin-Benito, M. Valle, J.M. Gonzalez, A. Valencia, J.M. Valpuesta, and J.L. Carrascosa Structure of the connector of bacteriophage T7 at 8 Å resolution: structural homologies of a basic component of a DNA translocating machinery J Mol Biol 347 2005 895 902 The isolated T7 phage connector structure was solved by cryo-EM. The protein fold and the 12-fold symmetry are similar to that of the φ29 phage connector crystal structure.
33. A.A. Simpson, Y. Tao, P.G. Leiman, M.O. Badasso, Y. He, P.J. Jardine, N.H. Olson, M.C. Morais, S. Grimes, and D.L. Anderson Structure of the bacteriophage phi29 DNA packaging motor Nature 408 2000 745 750
34. J.A. Briggs, J.T. Huiskonen, K.V. Fernando, R.J. Gilbert, P. Scotti, S.J. Butcher, and S.D. Fuller Classification and three-dimensional reconstruction of unevenly distributed or symmetry mismatched features of icosahedral particles J Struct Biol 150 2005 332 339 The authors demonstrate a method to solve the structure of non-icosahedral components of icosahedral particles. The method was applied to solve the structures of two different types of vertices of Kelp fly virus.
35. M.C. Morais, Y. Tao, N.H. Olson, S. Grimes, P.J. Jardine, D.L. Anderson, T.S. Baker, and M.G. Rossmann Cryoelectron-microscopy image reconstruction of symmetry mismatches in bacteriophage phi29 J Struct Biol 135 2001 38 46
36. Y. Cheng, O. Zak, P. Aisen, S.C. Harrison, and T. Walz Structure of the human transferrin receptor-transferrin complex Cell 116 2004 565 576
37. R. Matadeen, A. Patwardhan, B. Gowen, E.V. Orlova, T. Pape, M. Cuff, F. Mueller, R. Brimacombe, and M. van Heel The Escherichia coli large ribosomal subunit at 7.5 Å resolution Structure Fold Des 7 1999 1575 1583
38. M. Valle, A. Zavialov, W. Li, S.M. Stagg, J. Sengupta, R.C. Nielsen, P. Nissen, S.C. Harvey, M. Ehrenberg, and J. Frank Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy Nat Struct Biol 10 2003 899 906
39. J.F. Menetret, R.S. Hegde, S.U. Heinrich, P. Chandramouli, S.J. Ludtke, T.A. Rapoport, and C.W. Akey Architecture of the ribosome-channel complex derived from native membranes J Mol Biol 348 2005 445 457
40. 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
41. M. Unser, C.O. Sorzano, P. Thevenaz, S. Jonic, C. El-Bez, S. De Carlo, J.F. Conway, and B.L. Trus Spectral signal-to-noise ratio and resolution assessment of 3D reconstructions J Struct Biol 149 2005 243 255 In addition to proposing a new resolution criterion, the authors provide a good summary of the debate over resolution criteria.
42. P.A. Penczek Three-dimensional spectral signal-to-noise ratio for a class of reconstruction algorithms J Struct Biol 138 2002 34 46
43. A. Stewart, and N. Grigorieff Noise bias in the refinement of structures derived from single particles Ultramicroscopy 102 2004 67 84
44. S.J. Ludtke, I.I. Serysheva, S.L. Hamilton, and W. Chiu The pore structure of the closed RyR1 channel Structure 13 2005 1203 1211