Combining electron microscopic with X-ray crystallographic structures

Journal of Structural Biology

Volumn 136, Issue 3, 2001, Pages 190-200

  Rossmann, Michael G ^a   Bernal, Ricardo ^a   Pletnev, Sergei V ^a,b  

^a PURDUE UNIVERSITY   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Cryoelectron microscopy; Density fitting algorithm; Virus structures; X ray crystallography

Indexed keywords

DIMER; VIRUS GLYCOPROTEIN;

ALGORITHM; ARTICLE; ATOM; COMPUTER PROGRAM; CRYOELECTRON MICROSCOPY; DENGUE VIRUS; DENSITY; FLAVIVIRUS; IMAGE QUALITY; IMAGE RECONSTRUCTION; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; NONHUMAN; PARAMETER; PRIORITY JOURNAL; QUALITY CONTROL; THREE DIMENSIONAL IMAGING; VIRUS MORPHOLOGY; X RAY CRYSTALLOGRAPHY;

EID: 0035783056     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1006/jsbi.2002.4435     Document Type: Article

References (34)

1. Baker, T. S., and Johnson, J. E. (1996) Low resolution meets high: Towards a resolution continuum from cells to atoms. Curr. Opin. Struct. Biol. 6, 585-594.
2. Belnap, D. M., McDermott, B. M., Jr., Filman, D. J., Cheng, N., Trus, B. L., Zuccola, H. J., Racaniello, V. R., Hogle, J. M., and Steven, A. C. (2000) Three-dimensional structure of poliovirus receptor bound to poliovirus. Proc. Natl. Acad. Sci. USA 97, 73-78.
3. Böttcher, B., Wynne, S. A., and Crowther, R. A. (1997) Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature (London) 386, 88-91.
4. Caspar, D. L. D., and Klug, A. (1962) Physical principles in the construction of regular viruses. Cold Spring Harbor Symp. Quant. Biol. 27, 1-24.
5. Cheng, R. H., Kuhn, R. J., Olson, N. H., Rossmann, M. G., Choi, H. K., Smith, T. J., and Baker, T. S. (1995) Nucleocapsid and glycoprotein organization in an enveloped virus. Cell 80, 621-630.
6. Chiu, W., McGough, A., Sherman, M. B., and Schmid, M. F. (1999) High-resolution electron cryomicroscopy of macromolecular assemblies. Trends Cell Biol. 9, 154-159.
7. Conway, J. F., Cheng, N., Zlotnick, A., Wingfield, P. T., Stahl, S. J., and Steven, A. C. (1997) Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy. Nature (London) 386, 91-94.
8. Fuller, S. D., Berriman, J. A., Butcher, S. J., and Gowen, B. E. (1995) Low pH induces swiveling of the glycoprotein heterodimers in the Semliki Forest virus spike complex. Cell 81, 715-725.
9. Grimes, J. M., Jakana, J., Ghosh, M., Basak, A. K., Roy, P., Chiu, W., Stuart, D. I., and Prasad, B. V. V. (1997) An atomic model of the outer layer of the bluetongue virus core derived from X-ray crystallography and electron microscopy. Structure 5, 885-893.
10. He, Y., Bowman, V. D., Mueller, S., Bator, C. M., Bella, J., Peng, X., Baker, T. S., Wimmer, E., Kuhn, R. J., and Rossmann, M. G. (2000) Interaction of the poliovirus receptor with poliovirus. Proc. Natl. Acad. Sci. USA 97, 79-84.
11. He, Y., Chipman, P. R., Howitt, J., Bator, C. M., Whitt, M. A., Baker, T. S., Kuhn, R. J., Anderson, C. W., Freimuth, P., and Rossmann, M. G. (2001) Interaction of coxsackievirus B3 with the full-length coxsackievirus-adenovirus receptor. Nat. Struct. Biol. 8, 874-878.
12. Hewat, E. A., and Blaas, D. (1996) Structure of a neutralizing antibody bound bivalently to human rhinovirus 2. EMBO J. 15, 1515-1523.
13. Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. Sect. A 47, 110-119.
14. Kikkawa, M., Okada, Y., and Hirokawa, N. (2000) 15 Å resolution model of the monomeric kinesin motor, KIF1A. Cell 100, 241-252.
15. Kimura, Y., Vassylyev, D. G., Miyazawa, A., Kidera, A., Matsushima, M., Mitsuoka, K., Murata, K., Hirai, T., and Fujiyoshi, Y. (1997) Surface of bacteriorhodopsin revealed by high-resolution electron crystallography. Nature (London) 389, 206-211.
16. Kolatkar, P. R., Bella, J., Olson, N. H., Bator, C. M., Baker, T. S., and Rossmann, M. G. (1999) Structural studies of two rhinovirus serotypes complexed with fragments of their cellular receptor. EMBO J. 18, 6249-6259.
17. Kuhn, R. J., Zhang, W., Rossmann, M. G., Pletnev, S. V., Corver, J., Lenches, E., Jones, C. T., Mukhopadhyay, S., Chipman, P. R., Strauss, E. G., Baker, T. S., and Strauss, J. H. (2001) Structure of dengue virus: Implications for flavivirus organization, maturation, and fusion. Cell 108, 717-725.
18. Lescar, J., Roussel, A., Wein, M. W., Navaza, J., Fuller, S. D., Wengler, G., Wengler, G., and Rey, F. A. (2001) The fusion glycoprotein shell of Semliki Forest virus: An icosahedral assembly primed for fusogenic activation at endosomal pH. Cell 105, 137-148.
19. Mancini, E. J., Clarke, M., Gowen, B., Rutten, T., and Fuller, S. D. (2000) Cryo-electron microscopy reveals the functional anatomy of an enveloped virus, Semliki Forest virus. Mol. Cell 5, 255-266.
20. Pletnev, S. V., Zhang, W., Mukhopadhyay, S., Fisher, B. R., Hernandez, R., Brown, D. T., Baker, T. S., Rossmann, M. G., and Kuhn, R. J. (2001) Locations of carbohydrate sites on Sindbis virus glycoproteins show that E1 forms an icosahedral scaffold. Cell 105, 127-136.
21. Rey, F. A., Heinz, F. X., Mandl, C., Kunz, C., and Harrison, S. C. (1995) The envelope glycoprotein from tick-borne encephalitis virus at 2 Å resolution. Nature (London) 375, 291-298.
22. Roseman, A. M. (2000) Docking structures of domains into maps from cryo-electron microscopy using local correlation. Acta Crystallogr. Sect. D 56, 1332-1340.
23. Rossmann, M. G. (2000) Fitting atomic models into electron microscopy maps. Acta Crystallogr. Sect. D 56, 1341-1349.
24. Rossmann, M. G., and Blow, D. M. (1962) The detection of subunits within the crystallographic asymmetric unit. Acta Crystallogr. 15, 24-31.
25. Stewart, P. L., Fuller, S. D., and Burnett, R. M. (1993) Difference imaging of adenovirus: Bridging the resolution gap between X-ray crystallography and electron microscopy. EMBO J. 12, 2589-2599.
26. Thuman-Commike, P. A., and Chiu, W. (2000) Reconstruction principles of icosahedral virus structure determination using electron cryomicroscopy. Micron 31, 687-711.
27. 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. (2000) Single-particle electron cryo-microscopy: Towards atomic resolution. Q. Rev. Biophys. 33, 307-369.
28. Volkmann, N., Amann, K. J., Stoilova-McPhie, S., Egile, C., Winter, D. C., Hazelwood, L., Heuser, J. E., Li, R., Pollard, T. D., and Hanein, D. (2001) Structure of Arp2/3 complex in its activated state and in actin filament branch junctions. Science 293, 2456-2459.
29. Volkmann, N., and Hanein, D. (1999) Quantitative fitting of atomic models into observed densities derived by electron microscopy. J. Struct. Biol. 125, 176-184.
30. Wriggers, W., and Chacón, P. (2001) Modeling tricks and fitting techniques for multiresolution structures. Structure 9, 779-788.
31. Wriggers, W., Milligan, R. A., and McCammon, J. A. (1999) Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. J. Struct. Biol. 125, 185-189.
32. Xiao, C., Bator, C. M., Bowman, V. D., Rieder, E., He, Y., Hébert, B., Bella, J., Baker, T. S., Wimmer, E., Kuhn, R. J., and Rossmann, M. G. (2001) Interaction of coxsackievirus A21 with its cellular receptor, ICAM-1. J. Virol. 75, 2444-2451.
33. Zhou, Z. H., Baker, M. L., Jiang, W., Dougherty, M., Jakana, J., Dong, G., Lu, G., and Chiu, W. (2001) Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus. Nat. Struct. Biol. 8, 868-873.
34. Zhou, Z. H., Dougherty, M., Jakana, J., He, J., Rixon, F. J., and Chiu, W. (2000) Seeing the herpesvirus capsid at 8.5 Å. Science 288, 877-880.