Abstract
For about 30 years X-ray crystallography has been by far the most powerful approach for determining virus structures at close to atomic resolutions. Information provided by these studies has deeply and extensively enriched and shaped our vision of the virus world. In turn, the ever increasing complexity and size of the virus structures being investigated have constituted a major driving force for methodological and conceptual developments in X-ray macromolecular crystallography. Landmarks of new virus structures determinations, such as the ones from the first animal viruses or from the first membrane-containing viruses, have often been associated to methodological breakthroughs in X-ray crystallography. In this chapter we present the common ground of proteins and virus crystallography with an emphasis in the peculiarities of virus studies. For example, the solution of the phase problem, a central issue in X-ray diffraction, has benefited enormously from the presence of non-crystallographic symmetry in virus crystals.
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Abbreviations
- Ad:
-
Adenovirus
- Ad5:
-
Adenovirus type 5
- BTV:
-
Bluetongue virus
- EM:
-
Electron microscopy
- HRV2/HRV14:
-
Human rhinovirus serotypes 2 or 14
- MR:
-
Molecular replacement
- SBMV:
-
Southern bean mosaic virus
- STNV:
-
Satellite tobacco necrosis virus
- TBSV:
-
Tomato bushy stunt virus
- VLP:
-
Virus-like particle
References and Further Reading
Harrison SC, Olson AJ, Schutt CE, Winkler FK, Bricogne G (1978) Tomato bushy stunt virus at 2.9 A resolution. Nature 276:368–373
Abad-Zapatero C, Abdel-Meguid SS, Johnson JE, Leslie AG, Rayment I, Rossmann MG, Suck D, Tsukihara T (1980) Structure of southern bean mosaic virus at 2.8 A resolution. Nature 286:33–39
Liljas L, Unge T, Jones TA, Fridborg K, Lövgren S, Skoglund U, Strandberg B (1982) Structure of satellite tobacco necrosis virus at 3.0 A resolution. J Mol Biol 159:93–108
Verdaguer N, Blaas D, Fita I (2000) Structure of human rhinovirus serotype 2 (HRV2). J Mol Biol 300:1179–1194
Verdaguer N, Fita I, Reithmayer M, Moser R, Blaas D (2004) X-ray structure of a minor group human rhinovirus bound to a fragment of its cellular receptor protein. Nat Struct Mol Biol 11:429–434
Garriga D, Pickl-Herk A, Luque D, Wruss J, Castón JR, Blaas D, Verdaguer N (2012) Insights into minor group rhinovirus uncoating: the X-ray structure of the HRV2 empty capsid. PLoS Pathog 8:e1002473
Rossmann MG, Arnold E, Erickson JW et al (1985) Structure of a human common cold virus and functional relationship to other picornaviruses. Nature 317:145–153
Hogle JM, Chow M, Filman DJ (1985) Three-dimensional structure of poliovirus at 2.9 A resolution. Science 229:1358–1365
Grimes JM, Burroughs JN, Gouet P, Diprose JM, Malby R, Ziéntara S, Mertens PP, Stuart DI (1998) The atomic structure of the bluetongue virus core. Nature 395:470–478
Wilson IA, Skehel JJ, Wiley DC (1981) Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 Å resolution. Nature 289:366–373
Roberts MM, White JL, Grütter MG, Burnett RM (1986) Three-dimensional structure of the adenovirus major coat protein hexon. Science 232:1148–1151
Kwong PD, Wyatt R, Robinson J, Sweet RW, Sodroski J, Hendrickson WA (1998) Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature 393:648–659
Abrescia NG, Cockburn JJ, Grimes JM et al (2004) Insights into assembly from structural analysis of bacteriophage PRD1. Nature 432:68–74
Cockburn JJ, Abrescia NG, Grimes JM et al (2004) Membrane structure and interactions with protein and DNA in bacteriophage PRD1. Nature 2004(432):122–125
Reddy VS, Natchiar SK, Stewart PL, Nemerow GR (2010) Crystal structure of human adenovirus at 3.5 A resolution. Science 329:1071–1075
Stehle T, Casasnovas JM (2009) Specificity switching in virus-receptor complexes. Curr Opin Struct Biol 19:181–188
Ganser-Pornillos BK, Yeager M, Sundquist WI (2008) The structural biology of HIV assembly. Curr Opin Struct Biol 18:203–217
Harrison SC (2005) Mechanism of membrane fusion by viral envelope proteins. Adv Virus Res 64:231–261
Mukhopadhyay S, Kuhn RJ, Rossmann MG (2005) A structural perspective of the flavivirus life cycle. Nat Rev Microbiol 3:13–22
Wang X, Peng W, Ren J et al (2012) A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71. Nat Struct Mol Biol 19:424–429
Burzlaff H, Gruber B, Wolf PM et al (2002) Crystal lattices. In: Hahn T (ed) International tables for crystallography, vol A. Kluwer Academic Publishers, Dordrecht
Fry E, Grimes J, Stuart DI (1999) Virus crystallography. Mol Biotechnol 12:13–23
Fry E, Logan D, Stuart D (1996) Virus crystallography. In: Jones C, Mulloy B, Sanderson M (eds) Methods in molecular biology, vol 56: crystallographic methods and protocols. Humana Press, Totowa
Vijayachandran LS, Viola C, Garzoni F et al (2011) Robots, pipelines, polyproteins: enabling multiprotein expression in prokaryotic and eukaryotic cells. J Struct Biol 175:198–208
Chayen NE, Helliwell JR, Snell EH (2010) Macromolecular crystallization and crystal perfection. Oxford University Press, Oxford
Newman J (2005) Expanding screening space through the use of alternative reservoirs in vapor-diffusion experiments. Acta Crystallogr D Biol Crystallogr 61:490–493
Chayen NE (2005) Protein crystallization: automation robotization and miniaturization. In: Sundstrum M, Norin M, Edwards A (eds) Structural genomics and high throughput structural biology. CRC Press/Taylor & Francis, Abingdon
Garman E (2003) ‘Cool’ crystals: macromolecular cryocrystallography and radiation damage. Curr Opin Struct Biol 13:545–551
Mueller M, Jenni S, Ban N (2007) Strategies for crystallization and structure determination of very large macromolecular assemblies. Curr Opin Struct Biol 17:572–579
Cockburn JJ, Bamford JK, Grimes JM, Bamford DH, Stuart DI (2003) Crystallization of the membrane-containing bacteriophage PRD1 in quartz capillaries by vapour diffusion. Acta Crystallogr D Biol Crystallogr 59:538–540
Axford D, Owen RL, Aishima J et al (2012) In situ macromolecular crystallography using microbeams. Acta Crystallogr D Biol Crystallogr 68:592–600
Reinisch KM, Nibert ML, Harrison SC (2000) Structure of the reovirus core at 3.6 Å resolution. Nature 404:960–967
Gouet P, Diprose JM, Grimes JM et al (1999) The highly ordered double-stranded RNA Genome of bluetongue virus revealed by crystallography. Cell 97:481–490
Taka J, Naitow H, Yoshimura M, Miyazaki N, Nakagawa A, Tsukihara T (2005) Ab initio crystal structure determination of spherical viruses that exhibit a centrosymmetric location in the unit cell. Acta Crystallogr D Biol Crystallogr 61:1099–1106
Baker TS, Johnson JE (1997) Principles of virus structure determination. In: Chiu W, Burnett RM, Garcea RL (eds) Structural biology of viruses. Oxford University Press, New York
Arnold E, Vriend G, Luo M, Griffith JP, Kamer G, Erickson JW, Johnson JE, Rossmann MG (1987) The structure determination of a common cold virus, human rhinovirus 14. Acta Crystallogr A43:346–361
Fry E, Acharya R, Stuart D (1993) Methods used in the structure determination of foot-and-mouth disease virus. Acta Crystallogr A49:45–55
Speir JA, Munshi S, Wang G, Baker TS, Johnson JE (1995) Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryo-electron microscopy. Structure 3:63–78
Wynne SA, Crowther RA, Leslie AGW (1999) The crystal structure of the human hepatitis B virus capsid. Mol Cell 3:771–780
Tsao J, Chapman MS, Wu H, Agbandje M, Keller W, Rossmann MG (1992) Structure determination of monoclinic canine parvovirus. Acta Crystallogr B48:75–88
Arnold E, Rossmann MG (1985) Effect of errors, redundancy and solvent content in the molecular replacement procedure for the structure determination of biological macromolecules. PNAS 83:5489–5493
Rossmann MG (1989) The molecular replacement method. Acta Crystallogr A46:73–82
Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126–2132
Brunger AT, Kuriyan J, Karplus M (1987) Crystallographic R factor refinement by molecular dynamics. Science 235:458–460
Murshudov GN, Skubak P, Lebedev AA et al (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D67:355–367
Garriga D, Querol-Audí J, Abaitua F et al (2006) The 2.6-Angstrom structure of infectious bursal disease virus-derived T=1 particles reveals new stabilizing elements of the virus capsid. J Virol 80:6895–6905
Nandhagopal N, Simpson AA, Gurnon JR et al (2002) The structure and evolution of the major capsid protein of a large, lipid-containing DNA virus. PNAS 99:14758–14763
Zhanga X, Xianga Y, Duniganb DD et al (2011) Three-dimensional structure and function of the Paramecium bursaria chlorella virus capsid. PNAS 108:14837–14842
Abrescia NGA, Bamford DH, Grimes JM, Stuart DI (2012) Structure unifies the viral universe. Annu Rev Biochem 81:795–822
Raines KS, Salha S, Sanberg RL, Jiang H, Rodríguez JA, Fahimian B, Kapteyn HC, Du J, Miao J (2010) Three-dimensional structure determination from a single view. Nature 463:214–217
Seibert MM, Ekeberg T, Maia FR et al (2011) Single mimivirus particles intercepted and imaged with an X-ray laser. Nature 470:78–81
Further Reading
Blow D (2002) Outline of crystallography for biologists. Oxford University Press, Oxford
Rhodes G (2006) Crystallography made crystal clear, 3rd edn. Academic Press, London
Rupp B (2010) Macromolecular crystallography. Garland Science, Taylor & Francis group, LLC, New York
Acknowledgements
We would like to dedicate this chapter to Prof. M.G. Rossmann for his pioneering and continuous ground-breaking results in structural virology. This work was supported by grants from the Ministerio de Economia y Competitividad to N.V. (BIO2011-24333) and to I.F. (BFU2009-09268).
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Verdaguer, N., Garriga, D., Fita, I. (2013). X-Ray Crystallography of Viruses. In: Mateu, M. (eds) Structure and Physics of Viruses. Subcellular Biochemistry, vol 68. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6552-8_4
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