Classification and three-dimensional reconstruction of unevenly distributed or symmetry mismatched features of icosahedral particles

Journal of Structural Biology

Volumn 150, Issue 3, 2005, Pages 332-339

  Briggs, John A G ^a,d   Huiskonen, Juha T ^b   Fernando, K Vince ^a   Gilbert, Robert J C ^a   Scotti, Paul ^c   Butcher, Sarah J ^b   Fuller, Stephen D ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF HELSINKI   (Finland)

^c THE NEW ZEALAND INSTITUTE FOR PLANT AND FOOD RESEARCH LIMITED   (New Zealand)

^d UNIVERSITY OF MUNICH   (Germany)

Author keywords

Cryo electron microscopy; Icosahedral reconstruction; Partial occupancy; Symmetry mismatch; Virus

Indexed keywords

PROTEIN;

ARTICLE; CRYOELECTRON MICROSCOPY; DNA PACKAGING; FLY; KELP; MULTIVARIATE ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; THREE DIMENSIONAL IMAGING; VIRUS;

ALGORITHMS; CRYOELECTRON MICROSCOPY; DNA; GENOME, VIRAL; IMAGE PROCESSING, COMPUTER-ASSISTED; MICROSCOPY, ELECTRON; MODELS, STATISTICAL; MULTIVARIATE ANALYSIS; VIRION; VIRUS ASSEMBLY; VIRUSES;

COELOPIDAE;

EID: 18944398569     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jsb.2005.03.009     Document Type: Article

References (25)

1. T.S. Baker, and R.H. Cheng A model-based approach for determining orientations of biological macromolecules imaged by cryoelectron microscopy J. Struct. Biol. 116 1996 120 130
2. Baker, T.S., Olson, N.H., Fuller, S.D., 1999. Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs [published erratum appears in Microbiol. Mol. Biol. Rev. 2000 Mar;64(1):237]. Microbiol. Mol. Biol. Rev., 63, 862-922, table of contents
3. B. Böttcher, 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
4. M.E. Cerritelli, B.L. Trus, C.S. Smith, N. Cheng, J.F. Conway, and A.C. Steven A second symmetry mismatch at the portal vertex of bacteriophage T7: 8-fold symmetry in the procapsid core J. Mol. Biol. 327 2003 1 6
5. 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
6. R.A. Crowther Procedures for three-dimensional reconstruction of spherical viruses by Fourier synthesis from electron micrographs Philos. Trans. R Soc. Lond. B Biol. Sci. 261 1971 221 230
7. F. de Haas, A.O. Paatero, L. Mindich, D.H. Bamford, and S.D. Fuller A symmetry mismatch at the site of RNA packaging in the polymerase complex of dsRNA bacteriophage phi6 J. Mol. Biol. 294 1999 357 372
8. J. Frank, M. Radermacher, P. Penczek, J. Zhu, Y. Li, M. Ladjadj, and A. Leith SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields J. Struct. Biol. 116 1996 190 199
9. S.D. Fuller, S.J. Butcher, R.H. Cheng, and T.S. Baker Three-dimensional reconstruction of icosahedral particles-the uncommon line J. Struct. Biol. 116 1996 48 55
10. R.C. Gonzalez, and R.E. Woods Digital image processing 2002 Prentice Hall Upper Saddle River, New Jersey
11. J.B. Heymann Bsoft: image and molecular processing in electron microscopy J. Struct. Biol. 133 2001 156 169
12. J.T. Huiskonen, M.H. Kivelä, D.H. Bamford, and J B.S. 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. Ji, Y., Marinescu, D.C., Zhang, W., Baker, T.S., 2003. Orientation refinement of virus structures with unknown symmetry. Proc.17th Ann. Int'l Parallel & Distrib. Process. Symp. IEEE Press, Nice, France
14. A. Klug, and J.T. Finch Structure of viruses of the papilloma-polyoma type. IV. Analysis of tilting experiments in the electron microscope J. Mol. Biol. 31 1968 1 12
15. S.J. Ludtke, P.R. Baldwin, and W. Chiu EMAN: semiautomated software for high-resolution single-particle reconstructions J. Struct. Biol. 128 1999 82 97
16. E.J. Mancini, D.E. Kainov, J.M. Grimes, R. Tuma, D.H. Bamford, and D.I. Stuart Atomic snapshots of an RNA packaging motor reveal conformational changes linking ATP hydrolysis to RNA translocation Cell 118 2004 743 755
17. M.C. Morais, Y. Tao, N.H. Olson, S. Grimes, P.J. Jardine, D.L. Anderson, T.S. Baker, and M.G. Rossmann Cryo-electron microscopy image reconstruction of symmetry mismatches in bacteriophage φ29 J. Struct. Biol. 135 2001 38 46
18. E. Neumann, R. Moser, L. Snyers, D. Blaas, and E.A. Hewat A cellular receptor of human rhinovirus type 2, the very-low-density lipoprotein receptor, binds to two neighboring proteins of the viral capsid J. Virol. 77 2003 8504 8511
19. R.W. Ruigrok, A. Barge, S.K. Mittal, and B. Jacrot The fibre of bovine adenovirus type 3 is very long but bent J. Gen. Virol. 75 Pt. 8 1994 2069 2073
20. P.S. Rydman, J. Caldentey, S.J. Butcher, S.D. Fuller, T. Rutten, and D.H. Bamford Bacteriophage PRD1 contains a labile receptor-binding structure at each vertex J. Mol. Biol. 291 1999 575 587
21. P.L. Stewart, R.M. Burnett, M. Cyrklaff, and S.D. Fuller Image reconstruction reveals the complex molecular organization of adenovirus Cell 67 1991 145 154
22. E. Thouvenin, and E. Hewat When two into one won't go: fitting in the presence of steric hindrance and partial occupancy Acta Crystallogr. D Biol. Crystallogr. 56 Pt. 10 2000 1350 1357
23. M. van Heel Multivariate statistical classification of noisy images (randomly oriented biological macromolecules) Ultramicroscopy 13 1984 165 183
24. M. van Heel, B. Gowen, R. Matadeen, E.V. Orlova, R. Finn, T. Pape, D. Cohen, H. Stark, R. Schmidt, M. Schatz, and A. Patwardhan Single-particle electron cryo-microscopy: towards atomic resolution Q Rev. Biophys. 33 2000 307 369
25. M. van Heel, G. Harauz, E.V. Orlova, R. Schmidt, and M. Schatz A new generation of the IMAGIC image processing system J. Struct. Biol. 116 1996 17 24