Backbone trace of partitivi rus capsid protein from electron cryomicroscopy and homology modeling

Biophysical Journal

Volumn 99, Issue 2, 2010, Pages 685-694

  Tang, Jinghua ^a   Pan, Junhua ^c,f   Havens, Wendy M ^d   Ochoa, Wendji F ^a,g   Guu, Tom S Y ^c   Ghabrial, Said A ^d   Nibert, Max L ^e   Tao, Yizhi Jane ^c   Baker, Timothy S ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c RICE UNIVERSITY   (United States)

^d UNIVERSITY OF KENTUCKY   (United States)

^e HARVARD MEDICAL SCHOOL   (United States)

^f BOSTON CHILDREN S HOSPITAL   (United States)

^g BURNHAM INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAPSID PROTEIN;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CRYOELECTRON MICROSCOPY; GENETIC TRANSCRIPTION; GENETICS; MOLECULAR GENETICS; PARTICLE SIZE; PICOBIRNAVIRUS; PROTEIN MULTIMERIZATION; PROTEIN SECONDARY STRUCTURE; RABBIT; RNA VIRUS; STRUCTURAL HOMOLOGY; ULTRASTRUCTURE; VIRUS GENOME; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; ANIMALS; CAPSID PROTEINS; CRYOELECTRON MICROSCOPY; CRYSTALLOGRAPHY, X-RAY; GENOME, VIRAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PARTICLE SIZE; PICOBIRNAVIRUS; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, SECONDARY; RABBITS; RNA VIRUSES; STRUCTURAL HOMOLOGY, PROTEIN; TRANSCRIPTION, GENETIC;

EID: 77955222849     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.04.058     Document Type: Article

References (45)

1. Mertens, P. 2004. The dsRNA viruses. Virus Res. 104: 3-13.
2. Grimes, J. M., J. N. Burroughs, ..., D. I, Stuart. 1998. The atomic structure of the bluetongue virus core. Nature. 395: 470-478.
3. Naitow, H., J. Tang, ..., J. E. Johnson. 2002. L-A virus at 3.4 Å resolution reveals particle architecture and mRNA decapping mechanism. Nat. Struct. Biol. 9: 725-728.
4. Castón, J. R., S. A. Ghabrial, ..., J. L. Carrascosa. 2003. Three-dimensional structure of Penicillium chrysogenum virus: a double-stranded RNA virus with a genuine T=I capsid. J. Mol. Biol. 331: 417-431.
5. Coulibaly, F., C. Chevalier, ..., F. A. Rey. 2005. The birnavirus crystal structure reveals structural relationships among icosahedral viruses. Cell. 120: 761-772.
6. Huiskonen, J. T., F. de Haas, ..., S. J. Butcher. 2006. Structure of the bacteriophage Φ6 nucleocapsid suggests a mechanism for sequential RNA packaging. Structure. 14: 1039-1048.
7. Duquerroy, S., B. Da Costa, ..., F. A, Rey. 2009. The picobimavirus crystal structure provides functional insights into virion assembly and cell entry. EMBO J. 28: 1655-1665.
8. Pan, J., L. Dong, ..., Y. J. Tao. 2009. Atomic structure reveals the unique capsid organization of a dsRNA virus. Proc. Natl. Acad. Sci. USA. 106: 4225-4230.
9. Reinisch, K. M., M. L. Nibert, and S. C. Harrison. 2000. Structure of the reoviras core at 3.6 Å resolution. Nature. 404: 960-967.
10. Tao, Y., D. L. Farsetta, ..., S. C. Harrison. 2002. RNA synthesis in a cage - structural studies of reoviras polymerase λ3. Cell, 111: 733-745.
11. Bozarth, R. F., H. A. Wood, and A. Mandelbrot. 1971. The Penicillium stoloniferum virus complex: two similar double-stranded RNA viruslike particles in a single cell. Virology. 45: 516-523.
12. Banks, G. T., K. W. Buck, ..., O. M. Stone. 1968. Viruses in fungi and interferon stimulation. Nature. 218: 542-545.
13. Ghabrial, S. A., W. F. Ochoa, and M. L. Nibert. 2008. Partitiviruses: general features. In Encyclopedia of Virology., 3rd ed. B. W. J. Mahy and M. H. V. van Regenmortel, editors. Elsevier, Oxford. 68-75.
14. Buck, K. W., and G. F. Kempson-Jones. 1973. Biophysical properties of Pénicillium stoloniferum virus S. J. Gen. Virol. 18: 223-235.
15. Kim, J. W., S. Y. Kim, and K. M. Kim. 2003. Genome organization and expression of the Penicillium stoloniferum virus S. Virus Genes. 27: 249-256.
16. Kim, J. W., E. Y. Choi, and J. I, Lee. 2005. Genome organization and expression of the Penicillium stoloniferum virus F. Virus Genes. 31: 175-183.
17. Poirot, O., E. O'Toole, and C. Notredame. 2003. Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Res. 31: 3503-3506.
18. Buck, K. W., and G. F. Kempson-Jones. 1974. Capsid polypeptides of two viruses isolated from Penicillium stoloniferum. J. Gen. Virol. 22: 441-445.
19. Buck, K. W. 1978. Semi-conservative replication of double-stranded RNA by a virion-associated RNA polymerase. Biochem. Biophys. Res. Commun. 84: 639-645.
20. Ochoa, W. F., W. M. Havens, ..., T. S. Baker. 2008. Partitivirus structure reveals a 120-subunit, helix-rich capsid with distinctive surface arches formed by quasisymmetric coat-protein dimers. Structure. 16: 776-786.
21. Kuhn, R. J., W. Zhang, ..., J. H. Strauss. 2002. Structure of dengue virus: implications for flavivirus organization, maturation, and fusion. Cell. 108: 717-725.
22. Nakagawa, A., N. Miyazaki, ..., T. Tsukihara. 2003. The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins. Structure. 11: 1227-1238.
23. Jiang, W., M. L. Baker, ..., W. Chiu. 2008. Backbone structure of the infectious epsilon 15 virus capsid revealed by electron cryomicroscopy. Nature, 451: 1130-1134.
24. Ludtke, S. J., M. L. Baker, ..., W. Chiu. 2008. De novo backbone trace of GroEL from single particle electron, cryomicroscopy. Structure. 16: 441-448.
25. Yu, X., L. Jin, and Z. H. Zhou. 2008. 388 Å structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy. Nature. 453: 415-419.
26. Zhang, X., E. Setiembre, ..., N. Grigorieff. 2008. Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction. Proc. Natl. Acad. Sci. USA. 105: 1867-1872.
27. Suloway, C., J. Pulokas, ..., B. Carragher. 2005. Automated molecular microscopy: the new Leginon system. J. Struct. Biol. 151: 41-60.
28. Yan, X., R. S. Sinkovits, and T. S. Baker. 2007. AUTO3DEM - an automated and high throughput program for image reconstruction of icosahedral particles. J. Struct, Biol. 157: 73-82.
29. Bowman, V. D., E. S. Chase, ..., T. J. Smith. 2002. An antibody to the putative aphid recognition site on cucumber mosaic virus recognizes pentons but not hexons. J. Virol. 76: 12250-12258.
30. Zhang, X., Y. Ji, ..., T. S. Baker. 2005. Features of reoviras outer capsid protein μ1 revealed by electron cryomicroscopy and image reconstruction of the virion at 7.0 Å resolution, Structure, 13: 1545-1557.
31. van. Heel, M., and M. Schatz. 2005. Fourier shell correlation threshold criteria. J. Struct. Biol. 151: 250-262.
32. Havelka, W. A., R. Henderson, and D. Oesterhelt. 1995. Three-dimensional structure of halorhodopsin at 7 Å resolution. J. Mol. Biol. 247: 726-738.
33. Jones, T. A. 1992. A set of averaging programs. In Molecular Replacement. E. J. Dodson, S. Gover, and W. Wolf, editors. SERC Daresbury Laboratory, Warrington, UK. 91-105.
34. Collaborative Computational. Project No. 4. 1994. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50: 760-763.
35. Cole, C., J. D. Barber, and G. J. Barton. 2008. The JPred 3 secondary structure prediction server. Nucleic Acids Res. 36: W197-W201.
36. Brünger, A. T., P. D. Adams, ..., G. L. Warren. 1998. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54: 905-921.
37. Chapman, M. S. 1995. Restrained real-space macromolecular refinement using a new resolution-dependent electron density function. Acta Crystallogr. A. 51: 69-80.
38. Korostelev, A., R. Bertram, and M. S. Chapman. 2002. Simulated-annealing real-space refinement as a tool in model building. Acta Crystallogr. D Biol. Crystallogr. 58: 761-767.
39. Kleywegt, G. J., and R. J. Read. 1997. Not your average density. Structure. 5: 1557-1569.
40. Kraulis, P. 1991. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24: 946-950.
41. Goddard, T. D., C. C. Huang, and T. E. Ferrin. 2007. Visualizing density maps with UCSF Chimera. J. Struct. Biol. 157: 281-287.
42. Ji, Y., D. C. Marinescu, ..., T. S. Baker. 2006. A model-based parallel origin and orientation refinement algorithm for cryoTEM and its application to the study of virus structures. J. Struct. Biol, 154: 1-19.
43. Rosenthal, P. B., and R. Henderson. 2003. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333: 721-745.
44. Jones, T. A., J. Y. Zou, ..., M. Kjeldgaard. 1991. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A. 47: 110-119.
45. Zhang, X., S. B. Walker, ..., T. S. Baker. 2003. Reoviras polymerase λ3 localized by cryo-electron microscopy of virions at a resolution of 7.6 Å. Nat. Struct. Biol. 10: 1011-1018.