The crystallographic structure of Panicum Mosaic Virus (PMV)

Journal of Structural Biology

Volumn 181, Issue 1, 2013, Pages 37-52

  Makino, Debora L ^a   Larson, Steven B ^a   McPherson, Alexander ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Crystal structure; Icosahedral; NCS; Refinement; RNA; Tombusvirus; Virus crystallography; X ray

Indexed keywords

ASPARTIC ACID; CALCIUM ION; COAT PROTEIN; GENOMIC RNA; NUCLEOTIDE; VIRUS RNA;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; COCKSFOOT MOTTLE VIRUS; CONFORMATIONAL TRANSITION; NONHUMAN; PANICUM MOSAIC VIRUS; PLANT VIRUS; PRIORITY JOURNAL; PROTEIN RNA BINDING; PROTEIN SUBUNIT; TOBACCO NECROSIS VIRUS; VIRION; VIRUS GENOME; VIRUS MORPHOLOGY; VIRUS PARTICLE; X RAY CRYSTALLOGRAPHY; X RAY DIFFRACTION;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; CALCIUM; CAPSID PROTEINS; CONSERVED SEQUENCE; COORDINATION COMPLEXES; CRYSTALLOGRAPHY, X-RAY; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOSAIC VIRUSES; PANICUM; PROTEIN BINDING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RNA, VIRAL; STRUCTURAL HOMOLOGY, PROTEIN; SURFACE PROPERTIES; VIRION;

COCKSFOOT MOTTLE VIRUS; MIRIDAE; NECROVIRUS; PANICUM MOSAIC VIRUS; TOMBUSVIRUS;

EID: 84870891615     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2012.10.012     Document Type: Article

References (62)

1. Argos P., Johnson J.E. Chemical stability in simple plant viruses. Biological Macromolecules and Assemblies, Vol. I: Virus Structures 1984, 1-43. Wiley, New York. F.A. Jurnak, A. McPherson (Eds.).
2. Ban N., Larson S.B., McPherson A. Structural comparison of the plant satellite viruses. Virology 1995, 214:571-583.
3. Ban N., McPherson A. The structure of satellite panicum mosaic virus at 1.9å resolution. Nat. Struct. Biol. 1995, 2:882-890.
4. Barton G.J. Protein multiple sequence alignment and flexible pattern matching. Methods Enzymol. 1990, 183:403-428.
5. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., et al. The protein data bank. Nucleic Acids Res. 2000, 28:235-242.
6. Bhuvaneshwari M., Subramanya H.S., Gopinath K., Savithri H.S., Nayudu M.V., et al. Structure of sesbania mosaic virus at 3å resolution. Structure 1995, 3:1021-1030.
7. Brünger A.T. Version 1.2 of the crystallography and NMR system. Nat. Protoc. 2007, 2:2728-2733.
8. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D: Biol. Crystallogr. 1998, 54:905-921.
9. Buzen F.G., Niblett C.L., Hooper G.R., Hubbard J., Newman M.A. Further characterization of panicum mosaic virus and its associated satellite virus. Phytopathology 1984, 74:313-318.
10. Cabrera O., Scholthof K.B.G. The complex viral etiology of St. Augustine decline. Plant Dis. 1999, 83:902-904.
11. Canady M.A., Larson S.B., Day J., McPherson A. Crystal structure of turnip yellow mosaic virus. Nat. Struct. Biol. 1996, 3:771-781.
12. Cardoso J.M.S., Felix M.R., Clara M.I.E., Oliveira S. The complete genome sequence of a new necrovirus isolated from Olea europaea L. Arch. Virol. 2005, 150:815-823.
13. Carrillo-Tripp M., Shepherd C.M., Borelli A.I., Venkataraman S., et al. VIPERdb2: an enhanced and web API enabled relational database for structural virology. Nucleic Acid Res. 2009, 37:D436-D442.
14. Caspar D.L., Klug A. Physical principles in the construction of regular viruses. Cold Spring Harbor Symp. Quant. Biol. 1962, 27:1-24.
15. Chen Z., Stauffacher C., Li Y., Schmidt T., Bomer W., et al. Protein-RNA interactions in an icosahedral virus at 3.0å resolution. Science 1989, 245:154-159.
16. Day J., Ban N., Patel S., Larson S.B., McPherson A. Characterization of crystals of satellite panicum mosaic virus. J. Mol. Biol. 1994, 238:849-851.
17. DeLano W.L. The PYMOL Molecular Graphics System, v1.0r0 2002, DeLano Scientific, San Carlos, CA.
18. Emsley P., Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D: Biol. Crystallogr. 2004, 60:2126-2132.
19. Felix M.R., Cardoso J.M.S., Oliveira S., Clara M.I.E. Viral properties, primary structure and phylogenetic analysis of the coat protein of an olive latent virus 1 isolate from Olea europaea L. Virus Res. 2005, 108:195-198.
20. Fisher A.J., Johnson J.E. Ordered duplex RNA controls the capsid architecture of an icosahedral animal virus. Nature 1993, 361:176-179.
21. Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., et al. Protein identification and analysis tools on the ExPASy server. The Proteomics Protocols Handbook 2005, 571-607. Humana Press, New York. J.M. Walker (Ed.).
22. Henikoff S., Henikoff J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 1992, 89:10915-10919.
23. Hogle J.M., Maeda A., Harrison S.C. Structure and assembly of turnip crinkle virus 1. X-ray crystallographic structure-analysis at 3.2 å resolution. J. Mol. Biol. 1986, 191:625-638.
24. Hopper P., Harrison S.C., Sauer R.T. Structure of tomato bushy stunt virus. V. Coat protein sequence determination and its structural implications. J. Mol. Biol. 1984, 177:701-713.
25. Hosur M.V., Schmidt T., Tucker R.C., Johnson J.E., Gallagher T.M., et al. Structure of an insect virus at 3.0-å resolution. Proteins Struct. Funct. Genet. 1987, 2:167-176.
26. Johnson J.E., Argos P. Virus particle stability and structure. The Plant Viruses: Polyhedral Virions with Tripartite Genomes 1985, 19-56. Plenum Pres, New York. R.I.B. Francki (Ed.).
27. Johnson J.E., Rueckert R.R. Packaging and release of the viral genome. Structural Biology of Viruses 1997, 269-287. Oxford University Press, Oxford. W. Chiu, R.M. Burnett, R. Garcea (Eds.).
28. Jones T.A., Liljas L. Structure of satellite tobacco necrosis virus after crystallographic refinement at 2.5å resolution. J. Mol. Biol. 1984, 177:735-767.
29. Jones T.A., Zou J.Y., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A: Found. Crystallogr. 1991, 47:110-119.
30. Kaper, J.M., 1975. The Chemical Basis Of Virus Structure, Dissociation and Reassembly. North-Holland, Amsterdam, pp. 333-352.
31. Kleywegt G.J., Jones T.A. Software for handling macromolecular envelopes. Acta Crystallogr. D: Biol. Crystallogr. 1999, 55:941-944.
32. Lane S.W., Dennis C.A., Lane C.L., Trinh C.H., Rizkallah P.J., et al. Construction and crystal structure of recombinant STNV capsids. J. Mol. Biol. 2011, 413:41-50.
33. Larson S.B., Day J., Canady M.A., Greenwood A., McPherson A. Refined structure of desmodium yellow mottle tymovirus at 2.7 å resolution. J. Mol. Biol. 2000, 301:625-642.
34. Larson S.B., Day J., Greenwood A., McPherson A. Refined structure of satellite tobacco mosaic virus at 1.8å resolution. J. Mol. Biol. 1998, 277:37-59.
35. Larson S.B., Koszelak S., Day J., Greenwood A., Dodds J.A., et al. Double helical RNA in satellite tobacco mosaic virus. Nature 1993, 361:179-182.
36. Larson S.B., Lucas R.W., Greenwood A., McPherson A. The RNA of turnip yellow mosaic virus exhibits icosahedral order. Virology 2005, 334:245-254.
37. Larson S.B., Lucas R.W., McPherson A. Crystallographic structure of the T=1 particle of brome mosaic virus. J. Mol. Biol. 2005, 346:815-831.
38. Larson S.B., McPherson A. Satellite tobacco mosaic virus RNA: structure and implications for assembly. Curr. Opin. Struct. Biol. 2001, 11:59-65.
39. Makino D., Day J.S., Larson S.B., McPherson A. Investigation of RNA structure in satellite panicum mosaic virus. Virology 2006, 351:420-431.
40. Makino D.L., Larson S.B., McPherson A. Preliminary analysis of crystals of panicum mosaic virus (PMV) by X-ray diffraction and atomic force microscopy. Acta Crystallogr. D: Biol. Crystallogr. 2005, 61:173-179.
41. Masuta C., Zuidema D., Hunter B.G., Heaton L.A., Sopher D.S., et al. Analysis of the genome of satellite panicum mosaic virus. Virology 1987, 159:329-338.
42. Matthews B.W. Solvent content of protein crystals. J. Mol. Biol. 1968, 33:491-497.
43. McPherson A. Micelle formation and crystallization as paradigms for virus assembly. BioEssays 2005, 27:447-458.
44. Monis J., Sopher D.S., Jackson A.O. Biologically active cDNA clones of panicum mosaic virus satellites. Phytopathology 1992, 82:1175.
45. Morgunova E.Yu., Dauter Z., Fry E., Stuart D.I., Stel'mashchuk V.Ya. The atomic structure of carnation mottle virus capsid protein. FEBS Lett. 1994, 338:267-271.
46. Virus Taxonomy-Classification and Nomenclature of Viruses 1995, Springer-Verlag, Wien, New York. F.A. Murphy, C.M. Fauquet, D.H.L. Bishop, S.A. Ghabrial, A.W. Jarvis (Eds.).
47. Niblett C.L., Paulsen A.Q. Purification and further characterization of panicum mosaic virus. Phytopathology 1975, 65:1157-1160.
48. Nicholls A., Sharp K.A., Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 1991, 11:281-296.
49. Oda Y., Saeki K., Takahashi Y., Maeda T., Naitow H., et al. Crystal structure of tobacco necrosis virus at 2.25 å resolution. J. Mol. Biol. 2000, 300:153-169.
50. Pflugrath J.W. The finer things in X-ray diffraction data collection. Acta Crystallogr. D: Biol. Crystallogr. 1999, 55:1718-1725.
51. Read R.J. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A: Found. Crystallogr. 1986, 42:140-149.
52. Rossmann M.G., Arnold E. Non crystallographic symmetry averaging of electron density for molecular-replacement phase refinement and extension. vol. F 2001, 279-292. Kluwer Acad. Pub., London, UK. M.G. Rossmann, E. Arnold (Eds.).
53. Rossmann M.G., Erickson J.W. Structure and assembly of icosahedral shells. Virus Structure and Assembly 1985, 29-73. Jones & Bartlett Publishers, Boston. S. Casjens (Ed.).
54. Scholthof K.B.G. A synergism induced by satellite panicum mosaic virus. Mol. Plant-Microbe Interact. 1999, 12:163-166.
55. Silva A.M., Rossmann M.G. The refinement of southern bean mosaic virus in reciprocal space. Acta Crystallogr. B: Struct. Sci. 1985, 41:147-157.
56. Smith T.F., Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 1981, 147:195-197.
57. Speir J.A., Munshi S., Wang G.J., Baker T.S., Johnson J.E. Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryoelectron microscopy. Structure 1995, 3:63-78.
58. Tars K., Zeltins A., Liljas L. The three-dimensional structure of cocksfoot mottle virus at 2.7 å resolution. Virology 2003, 310:287-297.
59. Tsao J., Chapman M.S., Agbandje M., Keller W., Smith K., et al. The three dimensional structure of canine parvovirus and its functional implications. Science 1991, 251:1456-1464.
60. Turina M., Desvoyes B., Scholthof K.B.G. A gene cluster encoded by panicum mosaic virus is associated with virus movement. Virology 2000, 266:120-128.
61. Turina M., Maruoka M., Monis J., Jackson A.O., Scholthof K.B.G. Nucleotide sequence and infectivity of a full-length cDNA clone of panicum mosaic virus. Virology 1998, 241:141-155.
62. Zhang K.Y.J., Cowtan K.D., Main P. Phase improvement by iterative density modification. vol. F 2001, 321-324. Kluwer Acad. Pub., London, UK. M.G. Rossmann, E. Arnold (Eds.).