Combined Approaches to Study Virus Structures

  • Daniel Badia-Martinez
  • Hanna M. Oksanen
  • David I. Stuart
  • Nicola G. A. Abrescia
Part of the Subcellular Biochemistry book series (SCBI, volume 68)


A virus particle must work as a safe box for protecting its genome, but at the same time it has to undergo dramatic conformational changes in order to preserve itself by propagating in a cell infection. Thus, viruses are miniaturized wonders whose structural complexity requires them to be investigated by a combination of different techniques that can tackle both static and dynamic processes. In this chapter we will illustrate how major structural techniques such as X-ray crystallography and electron microscopy have been and can be combined with other techniques to determine the structure of complex viruses. The power of these hybrid method approaches are revealed through the various examples provided.


Hybrid methods X-ray crystallography Electron microscopy Cryo-electron microscopy Electron tomography Cryo-electron tomography Small-angle X-ray scattering Virus Bacteriophage Capsid Mutagenesis Dissociation Crystal structure Fitting 



Two dimensional


Three dimensional


Bromegrass mosaic virus


Electron microscopy


Electron tomography


Antigen-binding antibody fragment


Foot-and-mouth disease virus


Hepatitis C virus


HCV-like particle


Human immunodeficiency virus


Human rhinovirus 16


Herpes simplex virus


Molecular replacement


Non-crystallographic symmetry


Nuclear magnetic resonance


Rift Valley fever virus


Small-angle neutron scattering


Small-angle X-ray scattering


Southern bean mosaic virus




Simian immunodeficiency virus


Tomato bushy stunt virus


Transmission electron microscopy


Tobacco mosaic virus


Tobacco necrosis virus


Virus-like particle


West Nile virus

References and Further Reading

  1. 1.
    Harrison SC, Olson AJ, Schutt CE, Winkler FK, Bricogne G (1978) Tomato bushy stunt virus at 2.9 Å resolution. Nature 276:368–373PubMedCrossRefGoogle Scholar
  2. 2.
    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 2.8Å resolution. Nature 286:33–39PubMedCrossRefGoogle Scholar
  3. 3.
    Roberts MM, White JL, Grutter MG, Burnett RM (1986) Three-dimensional structure of the adenovirus major coat protein hexon. Science 232:1148–1151PubMedCrossRefGoogle Scholar
  4. 4.
    Goldsmith CS, Miller SE (2009) Modern uses of electron microscopy for detection of viruses. Clin Microbiol Rev 22:552–563PubMedCrossRefGoogle Scholar
  5. 5.
    Jiang W, Baker ML, Jakana J, Weigele PR, King J, Chiu W (2008) Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy. Nature 451:1130–1134PubMedCrossRefGoogle Scholar
  6. 6.
    Hagen C, Guttmann P, Klupp B, Werner S, Rehbein S, Mettenleiter TC, Schneider G, Grünewald K (2012) Correlative VIS-fluorescence and soft X-ray cryo-microscopy/tomography of adherent cells. J Struct Biol 177:193–201PubMedCrossRefGoogle Scholar
  7. 7.
    Svergun DI, Koch MH (2003) Small-angle scattering studies of biological macromolecules in solution. Rep Prog Phys 66:1735–1782CrossRefGoogle Scholar
  8. 8.
    Svergun DI, Koch MH (2002) Advances in structure analysis using small-angle scattering in solution. Curr Opin Struct Biol 12:654–660PubMedCrossRefGoogle Scholar
  9. 9.
    Stubbs G (2001) Fibre diffraction studies of filamentous viruses. Rep Prog Phys 64:1389–1425CrossRefGoogle Scholar
  10. 10.
    Harrison SC, Caspar DL, Camerini-Otero RD, Franklin RM (1971) Lipid and protein arrangement in bacteriophage PM2. Nat New Biol 229:197–201PubMedGoogle Scholar
  11. 11.
    Abrescia NG, Grimes JM, Kivela HM, Assenberg R, Sutton GC, Butcher SJ, Bamford JK, Bamford DH, Stuart DI (2008) Insights into virus evolution and membrane biogenesis from the structure of the marine lipid-containing bacteriophage PM2. Mol Cell 31:749–761PubMedCrossRefGoogle Scholar
  12. 12.
    Canady MA, Tsuruta H, Johnson JE (2001) Analysis of rapid, large-scale protein quaternary structural changes: time-resolved X-ray solution scattering of Nudaurelia capensis omega virus (NomegaV) maturation. J Mol Biol 311:803–814PubMedCrossRefGoogle Scholar
  13. 13.
    Fry EE, Abrescia NGA, Stuart DI (2007) Virus crystallography. In: Sanderson M, Skelly J (eds) Macromolecular crystallography: conventional and high-throughput methods – a practical approach. Oxford University Press, OxfordGoogle Scholar
  14. 14.
    Tuthill TJ, Harlos K, Walter TS, Knowles NJ, Groppelli E, Rowlands DJ, Stuart DI, Fry EE (2009) Equine rhinitis A virus and its low pH empty particle: clues towards an aphthovirus entry mechanism? PLoS Pathog 5:e1000620PubMedCrossRefGoogle Scholar
  15. 15.
    Hogle JM, Chow M, Filman DJ (1985) Three-dimensional structure of poliovirus at 2.9 A resolution. Science 229:1358–1365PubMedCrossRefGoogle Scholar
  16. 16.
    Rossmann MG, Arnold E, Erickson JW, Frankenberger EA, Griffith JP, Hecht H, Johnson JJ, Kamer G, Luo M, Mosser AG, Rueckert RR, Sherry B, Vriend G (1985) Structure of a human common cold virus and functional relationship to other picornaviruses. Nature 317:145–153PubMedCrossRefGoogle Scholar
  17. 17.
    Abrescia NG, Cockburn JJ, Grimes JM, Sutton GC, Diprose JM, Butcher SJ, Fuller SD, San Martín C, Burnett RM, Stuart DI, Bamford DH, Bamford JK (2004) Insights into assembly from structural analysis of bacteriophage PRD1. Nature 432:68–74PubMedCrossRefGoogle Scholar
  18. 18.
    Cockburn JJ, Abrescia NG, Grimes JM, Sutton GC, Diprose JM, Benevides JM, Thomas GJ Jr, Bamford JK, Bamford DH, Stuart DI (2004) Membrane structure and interactions with protein and DNA in bacteriophage PRD1. Nature 432:122–125PubMedCrossRefGoogle Scholar
  19. 19.
    Liu H, Jin L, Koh SB, Atanasov I, Schein S, Wu L, Zhou ZH (2010) Atomic structure of human adenovirus by cryo-EM reveals interactions among protein networks. Science 329:1038–1043PubMedCrossRefGoogle Scholar
  20. 20.
    Reddy VS, Natchiar SK, Stewart PL, Nemerow GR (2010) Crystal structure of human adenovirus at 3.5 A resolution. Science 329:1071–1075PubMedCrossRefGoogle Scholar
  21. 21.
    Perrakis A, Daenke S, Stuart DI, Sussman JL (2011) From SPINE to SPINE-2 complexes and beyond. J Struct Biol 175:105PubMedCrossRefGoogle Scholar
  22. 22.
    Axford D, Owen RL, Aishima J, Foadi J, Morgan AW, Robinson JI, Nettleship JE, Owens RJ, Moraes I, Fry EE, Grimes JM, Harlos K, Kotecha A, Ren J, Sutton G, Walter TS, Stuart DI, Evans G (2012) In situ macromolecular crystallography using microbeams. Acta Crystallogr D Biol Crystallogr 68:592–600PubMedCrossRefGoogle Scholar
  23. 23.
    Wang X, Peng W, Ren J, Hu Z, Xu J, Lou Z, Li X, Yin W, Shen X, Porta C, Walter TS, Evans G, Axford D, Owen R, Rowlands DJ, Wang J, Stuart DI, Fry EE, Rao Z (2012) A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71. Nat Struct Mol Biol 19:424–429PubMedCrossRefGoogle Scholar
  24. 24.
    Evans G, Axford D, Owen RL (2011) The design of macromolecular crystallography diffraction experiments. Acta Crystallogr D Biol Crystallogr 67:261–270PubMedCrossRefGoogle Scholar
  25. 25.
    Rossmann MG (2000) Fitting atomic models into electron-microscopy maps. Acta Crystallogr D Biol Crystallogr 56:1341–1349PubMedCrossRefGoogle Scholar
  26. 26.
    Kolatkar PR, Bella J, Olson NH, Bator CM, Baker TS, Rossmann MG (1999) Structural studies of two rhinovirus serotypes complexed with fragments of their cellular receptor. EMBO J 18:6249–6259PubMedCrossRefGoogle Scholar
  27. 27.
    Gilbert RJ, Grimes JM, Stuart DI (2003) Hybrid vigor: hybrid methods in viral structure determination. Adv Protein Chem 64:37–91PubMedCrossRefGoogle Scholar
  28. 28.
    Topf M, Sali A (2005) Combining electron microscopy and comparative protein structure modeling. Curr Opin Struct Biol 15:578–585PubMedCrossRefGoogle Scholar
  29. 29.
    Kaufmann KW, Lemmon GH, Deluca SL, Sheehan JH, Meiler J (2010) Practically useful: what the Rosetta protein modeling suite can do for you. Biochemistry 49:2987–2998PubMedCrossRefGoogle Scholar
  30. 30.
    Franklin RE, Harrison SC, Pettersson U, Philipson L, Branden CJ, Werner P (1971) Structural studies on the adenovirus hexon. Cold Spring Harb Symp Quant Biol 36:503–510CrossRefGoogle Scholar
  31. 31.
    Hewat EA, Verdaguer N, Fita I, Blakemore W, Brookes S, King A, Newman J, Domingo E, Mateu MG, Stuart DI (1997) Structure of the complex of an Fab fragment of a neutralizing antibody with foot-and-mouth disease virus: positioning of a highly mobile antigenic loop. EMBO J 16:1492–1500PubMedCrossRefGoogle Scholar
  32. 32.
    Yu IM, Zhang W, Holdaway HA, Li L, Kostyuchenko VA, Chipman PR, Kuhn RJ, Rossmann MG, Chen J (2008) Structure of the immature dengue virus at low pH primes proteolytic maturation. Science 319:1834–1837PubMedCrossRefGoogle Scholar
  33. 33.
    Li L, Lok SM, Yu IM, Zhang Y, Kuhn RJ, Chen J, Rossmann MG (2008) The flavivirus precursor membrane-envelope protein complex: structure and maturation. Science 319:1830–1834PubMedCrossRefGoogle Scholar
  34. 34.
    Cherrier MV, Kaufmann B, Nybakken GE, Lok SM, Warren JT, Chen BR, Nelson CA, Kostyuchenko VA, Holdaway HA, Chipman PR, Kuhn RJ, Diamond MS, Rossmann MG, Fremont DH (2009) Structural basis for the preferential recognition of immature flaviviruses by a fusion-loop antibody. EMBO J 28:3269–3276PubMedCrossRefGoogle Scholar
  35. 35.
    Bamford DH, Caldentey J, Bamford JK (1995) Bacteriophage PRD1: a broad host range dsDNA tectivirus with an internal membrane. Adv Virus Res 45:281–319PubMedCrossRefGoogle Scholar
  36. 36.
    San Martin C, Burnett RM, de Haas F, Heinkel R, Rutten T, Fuller SD, Butcher SJ, Bamford DH (2001) Combined EM/X-Ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions. Structure 9:917–930CrossRefGoogle Scholar
  37. 37.
    Benson SD, Bamford JK, Bamford DH, Burnett RM (1999) Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures. Cell 98:825–833PubMedCrossRefGoogle Scholar
  38. 38.
    Bamford DH, Burnett RM, Stuart DI (2002) Evolution of viral structure. Theor Popul Biol 61:461–470PubMedCrossRefGoogle Scholar
  39. 39.
    Nickell S, Forster F, Linaroudis A, Net WD, Beck F, Hegerl R, Baumeister W, Plitzko JM (2005) TOM software toolbox: acquisition and analysis for electron tomography. J Struct Biol 149:227–234PubMedCrossRefGoogle Scholar
  40. 40.
    Scheres SH, Melero R, Valle M, Carazo JM (2009) Averaging of electron subtomograms and random conical tilt reconstructions through likelihood optimization. Structure 17:1563–1572PubMedCrossRefGoogle Scholar
  41. 41.
    Castaño-Diez D, Kudryashev M, Arheit M, Stahlberg H (2012) Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments. J Struct Biol 178:139–151PubMedCrossRefGoogle Scholar
  42. 42.
    Briggs JA, Riches JD, Glass B, Bartonova V, Zanetti G, Kräusslich HG (2009) Structure and assembly of immature HIV. Proc Natl Acad Sci U S A 106:11090–11095PubMedCrossRefGoogle Scholar
  43. 43.
    Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Sali A, Rout MP (2007) The molecular architecture of the nuclear pore complex. Nature 450:695–701PubMedCrossRefGoogle Scholar
  44. 44.
    Brunger AT (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355:472–475PubMedCrossRefGoogle Scholar
  45. 45.
    Tsao J, Chapman MS, Rossmann MG (1992) Ab initio phase determination for viruses with high symmetry: a feasibility study. Acta Crystallogr A 48(Pt 3):293–301PubMedCrossRefGoogle Scholar
  46. 46.
    Chapman MS, Tsao J, Rossmann MG (1992) Ab initio phase determination for spherical viruses: parameter determination for spherical-shell models. Acta Crystallogr A 48(Pt 3):301–312PubMedCrossRefGoogle Scholar
  47. 47.
    Rossmann MG (1995) Ab initio phase determination and phase extension using non-crystallographic symmetry. Curr Opin Struct Biol 5:650–655PubMedCrossRefGoogle Scholar
  48. 48.
    Rossmann MG (1990) The molecular replacement method. Acta Crystallogr A 46(Pt 2):73–82PubMedCrossRefGoogle Scholar
  49. 49.
    Acharya R, Fry E, Stuart D, Fox G, Rowlands D, Brown F (1989) The three-dimensional structure of foot-and-mouth disease virus at 2.9 Å resolution. Nature 337:709–716PubMedCrossRefGoogle Scholar
  50. 50.
    Villeret V, Tricot C, Stalon V, Dideberg O (1995) Crystal structure of Pseudomonas aeruginosa catabolic ornithine transcarbamoylase at 3.0 Å resolution: a different oligomeric organization in the transcarbamoylase family. Proc Natl Acad Sci U S A 92:10762–10766PubMedCrossRefGoogle Scholar
  51. 51.
    Dodson EJ (2001) Using electron-microscopy images as a model for molecular replacement. Acta Crystallogr D Biol Crystallogr 57:1405–1409PubMedCrossRefGoogle Scholar
  52. 52.
    Navaza J (2008) Combining X-ray and electron-microscopy data to solve crystal structures. Acta Crystallogr D Biol Crystallogr 64:70–75PubMedCrossRefGoogle Scholar
  53. 53.
    Trapani S, Schoehn G, Navaza J, Abergel C (2010) Macromolecular crystal data phased by negative-stained electron-microscopy reconstructions. Acta Crystallogr D Biol Crystallogr 66:514–521PubMedCrossRefGoogle Scholar
  54. 54.
    Hao Q, Dodd FE, Grossmann JG, Hasnain SS (1999) Ab initio phasing using molecular envelope from solution X-ray scattering. Acta Crystallogr D Biol Crystallogr 55:243–246PubMedCrossRefGoogle Scholar
  55. 55.
    Huiskonen JT, Kivelä HM, Bamford DH, Butcher SJ (2004) The PM2 virion has a novel organization with an internal membrane and pentameric receptor binding spikes. Nat Struct Mol Biol 11:850–856PubMedCrossRefGoogle Scholar
  56. 56.
    Abrescia NG, Grimes JM, Oksanen HM, Bamford JK, Bamford DH, Stuart DI (2011) The use of low-resolution phasing followed by phase extension from 7.6 to 2.5 Å resolution with noncrystallographic symmetry to solve the structure of a bacteriophage capsid protein. Acta Crystallogr D Biol Crystallogr 67:228–232PubMedCrossRefGoogle Scholar
  57. 57.
    Abrescia NG, Kivelä HM, Grimes JM, Bamford JK, Bamford DH, Stuart DI (2005) Preliminary crystallographic analysis of the major capsid protein P2 of the lipid-containing bacteriophage PM2. Acta Crystallogr Sect F Struct Biol Cryst Commun 61:762–765PubMedCrossRefGoogle Scholar
  58. 58.
    Leitner A, Reischl R, Walzthoeni T, Herzog F, Bohn S, Förster F, Aebersold R (2012) Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography. Mol Cell Proteomics 11(M111):014126PubMedGoogle Scholar
  59. 59.
    Gowen B, Bamford JK, Bamford DH, Fuller SD (2003) The tailless icosahedral membrane virus PRD1 localizes the proteins involved in genome packaging and injection at a unique vertex. J Virol 77:7863–7871PubMedCrossRefGoogle Scholar
  60. 60.
    Strömsten NJ, Bamford DH, Bamford JK (2003) The unique vertex of bacterial virus PRD1 is connected to the viral internal membrane. J Virol 77:6314–6321PubMedCrossRefGoogle Scholar
  61. 61.
    Kivelä HM, Madonna S, Krupovic M, Tutino ML, Bamford JK (2008) Genetics for Pseudoalteromonas provides tools to manipulate marine bacterial virus PM2. J Bacteriol 190:1298–1307PubMedCrossRefGoogle Scholar
  62. 62.
    Avilov SV, Moisy D, Munier S, Schraidt O, Naffakh N, Cusack S (2011) Replication-competent influenza A virus that encodes a split-green fluorescent protein-tagged PB2 polymerase subunit allows live-cell imaging of the virus life cycle. J Virol 86:1433–1448PubMedCrossRefGoogle Scholar
  63. 63.
    Kivelä HM, Abrescia NG, Bamford JK, Grimes JM, Stuart DI, Bamford DH (2008) Selenomethionine labeling of large biological macromolecular complexes: probing the structure of marine bacterial virus PM2. J Struct Biol 161:204–210PubMedCrossRefGoogle Scholar
  64. 64.
    Bamford D, Mindich L (1982) Structure of the lipid-containing bacteriophage PRD1: disruption of wild-type and nonsense mutant phage particles with guanidine hydrochloride. J Virol 44:1031–1038PubMedGoogle Scholar
  65. 65.
    Kivelä HM, Kalkkinen N, Bamford DH (2002) Bacteriophage PM2 has a protein capsid surrounding a spherical proteinaceous lipid core. J Virol 76:8169–8178PubMedCrossRefGoogle Scholar
  66. 66.
    Caldentey J, Luo C, Bamford DH (1993) Dissociation of the lipid-containing bacteriophage PRD1: effects of heat, pH, and sodium dodecyl sulfate. Virology 194:557–563PubMedCrossRefGoogle Scholar
  67. 67.
    Kivelä HM, Roine E, Kukkaro P, Laurinavicius S, Somerharju P, Bamford DH (2006) Quantitative dissociation of archaeal virus SH1 reveals distinct capsid proteins and a lipid core. Virology 356:4–11PubMedCrossRefGoogle Scholar
  68. 68.
    Pietilä MK, Atanasova NS, Manole V, Liljeroos L, Butcher SJ, Oksanen HM, Bamford DH (2012) Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea. J Virol 86:5067–5079PubMedCrossRefGoogle Scholar
  69. 69.
    Rissanen I, Pawlowski A, Harlos K, Grimes JM, Stuart DI, Bamford JKH (2012) Crystallization and preliminary crystallographic analysis of the major capsid proteins VP16 and VP17 of bacteriophage P23-77. Acta Crystallogr F68:580–583Google Scholar
  70. 70.
    Aricescu AR, Lu W, Jones EY (2006) A time- and cost-efficient system for high-level protein production in mammalian cells. Acta Crystallogr D Biol Crystallogr 62:1243–1250PubMedCrossRefGoogle Scholar
  71. 71.
    Benson SD, Bamford JK, Bamford DH, Burnett RM (2002) The X-ray crystal structure of P3, the major coat protein of the lipid-containing bacteriophage PRD1, at 1.65 A resolution. Acta Crystallogr D Biol Crystallogr 58:39–59PubMedCrossRefGoogle Scholar
  72. 72.
    Hendrickson WA (1991) Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science 254:51–58PubMedCrossRefGoogle Scholar
  73. 73.
    Jeembaeva M, Jonsson B, Castelnovo M, Evilevitch A (2010) DNA heats up: energetics of genome ejection from phage revealed by isothermal titration calorimetry. J Mol Biol 395:1079–1087PubMedCrossRefGoogle Scholar
  74. 74.
    Walter TS, Ren J, Tuthill TJ, Rowlands DJ, Stuart DI, Fry EE (2012) A plate-based high throughput assay for virus stability and vaccine formulation. J Virol Methods 185(1):166–170PubMedCrossRefGoogle Scholar
  75. 75.
    Shoemaker GK, van Duijn E, Crawford SE, Uetrecht C, Baclayon M, Roos WH, Wuite GJ, Estes MK, Prasad BV, Heck AJ (2010) Norwalk virus assembly and stability monitored by mass spectrometry. Mol Cell Proteomics 9:1742–1751PubMedCrossRefGoogle Scholar
  76. 76.
    Lucic V, Forster F, Baumeister W (2005) Structural studies by electron tomography: from cells to molecules. Annu Rev Biochem 74:833–865PubMedCrossRefGoogle Scholar
  77. 77.
    Subramaniam S, Bartesaghi A, Liu J, Bennett AE, Sougrat R (2007) Electron tomography of viruses. Curr Opin Struct Biol 17:596–602PubMedCrossRefGoogle Scholar
  78. 78.
    Freiberg AN, Sherman MB, Morais MC, Holbrook MR, Watowich SJ (2008) Three-dimensional organization of Rift Valley fever virus revealed by cryoelectron tomography. J Virol 82:10341–10348PubMedCrossRefGoogle Scholar
  79. 79.
    Grünewald K, Desai P, Winkler DC, Heymann JB, Belnap DM, Baumeister W, Steven AC (2003) Three-dimensional structure of herpes simplex virus from cryo-electron tomography. Science 302:1396–1398PubMedCrossRefGoogle Scholar
  80. 80.
    Bowman BR, Baker ML, Rixon FJ, Chiu W, Quiocho FA (2003) Structure of the herpesvirus major capsid protein. EMBO J 22:757–765PubMedCrossRefGoogle Scholar
  81. 81.
    Baker ML, Jiang W, Rixon FJ, Chiu W (2005) Common ancestry of herpesviruses and tailed DNA bacteriophages. J Virol 79:14967–14970PubMedCrossRefGoogle Scholar
  82. 82.
    Bostina M, Bubeck D, Schwartz C, Nicastro D, Filman DJ, Hogle JM (2007) Single particle cryoelectron tomography characterization of the structure and structural variability of poliovirus-receptor-membrane complex at 30 A resolution. J Struct Biol 160:200–210PubMedCrossRefGoogle Scholar
  83. 83.
    Zhu P, Liu J, Bess J Jr, Chertova E, Lifson JD, Grisé H, Ofek GA, Taylor KA, Roux KH (2006) Distribution and three-dimensional structure of AIDS virus envelope spikes. Nature 441:847–852PubMedCrossRefGoogle Scholar
  84. 84.
    Zanetti G, Briggs JA, Grünewald K, Sattentau QJ, Fuller SD (2006) Cryo-electron tomographic structure of an immunodeficiency virus envelope complex in situ. PLoS Pathog 2:e83PubMedCrossRefGoogle Scholar
  85. 85.
    Chen B, Vogan EM, Gong H, Skehel JJ, Wiley DC, Harrison SC (2005) Structure of an unliganded simian immunodeficiency virus gp120 core. Nature 433:834–841PubMedCrossRefGoogle Scholar
  86. 86.
    Liu J, Bartesaghi A, Borgnia MJ, Sapiro G, Subramaniam S (2008) Molecular architecture of native HIV-1 gp120 trimers. Nature 455:109–113PubMedCrossRefGoogle Scholar
  87. 87.
    Harris A, Cardone G, Winkler DC, Heymann JB, Brecher M, White JM, Steven AC (2006) Influenza virus pleiomorphy characterized by cryoelectron tomography. Proc Natl Acad Sci U S A 103:19123–19127PubMedCrossRefGoogle Scholar
  88. 88.
    Huiskonen JT, Overby AK, Weber F, Grünewald K (2009) Electron cryo-microscopy and single-particle averaging of Rift Valley fever virus: evidence for GN-GC glycoprotein heterodimers. J Virol 83:3762–3769PubMedCrossRefGoogle Scholar
  89. 89.
    Carrascosa JL, Chichon FJ, Pereiro E, Rodriguez MJ, Fernandez JJ, Esteban M, Heim S, Guttmann P, Schneider G (2009) Cryo-X-ray tomography of vaccinia virus membranes and inner compartments. J Struct Biol 168:234–239PubMedCrossRefGoogle Scholar
  90. 90.
    Ji X, Sutton G, Evans G, Axford D, Owen R, Stuart DI (2009) How baculovirus polyhedra fit square pegs into round holes to robustly package viruses. EMBO J 29:505–514PubMedCrossRefGoogle Scholar
  91. 91.
    Koopmann R, Cupelli K, Redecke L, Nass K, Deponte DP, White TA, Stellato F, Rehders D, Liang M, Andreasson J, Aquila A, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Boutet S, Bozek JD, Caleman C, Coppola N, Davidsson J, Doak RB, Ekeberg T, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann A, Hartmann R, Hauser G, Hirsemann H, Holl P, Hunter MS, Kassemeyer S, Kirian RA, Lomb L, Maia FR, Kimmel N, Martin AV, Messerschmidt M, Reich C, Rolles D, Rudek B, Rudenko A, Schlichting I, Schulz J, Seibert MM, Shoeman RL, Sierra RG, Soltau H, Stern S, Strüder L, Timneanu N, Ullrich J, Wang X, Weidenspointner G, Weierstall U, Williams GJ, Wunderer CB, Fromme P, Spence JC, Stehle T, Chapman HN, Betzel C, Duszenko M (2012) In vivo protein crystallization opens new routes in structural biology. Nat Methods 9:259–262PubMedCrossRefGoogle Scholar
  92. 92.
    Iwasaki K, Omura T (2010) Electron tomography of the supramolecular structure of virus-infected cells. Curr Opin Struct Biol 20:632–639PubMedCrossRefGoogle Scholar
  93. 93.
    Chapman HN, Fromme P, Barty A, White TA, Kirian RA, Aquila A, Hunter MS, Schulz J, DePonte DP, Weierstall U, Doak RB, Maia FR, Martin AV, Schlichting I, Lomb L, Coppola N, Shoeman RL, Epp SW, Hartmann R, Rolles D, Rudenko A, Foucar L, Kimmel N, Weidenspointner G, Holl P, Liang M, Barthelmess M, Caleman C, Boutet S, Bogan MJ, Krzywinski J, Bostedt C, Bajt S, Gumprecht L, Rudek B, Erk B, Schmidt C, Hömke A, Reich C, Pietschner D, Strüder L, Hauser G, Gorke H, Ullrich J, Herrmann S, Schaller G, Schopper F, Soltau H, Kühnel KU, Messerschmidt M, Bozek JD, Hau-Riege SP, Frank M, Hampton CY, Sierra RG, Starodub D, Williams GJ, Hajdu J, Timneanu N, Seibert MM, Andreasson J, Rocker A, Jönsson O, Svenda M, Stern S, Nass K, Andritschke R, Schröter CD, Krasniqi F, Bott M, Schmidt KE, Wang X, Grotjohann I, Holton JM, Barends TR, Neutze R, Marchesini S, Fromme R, Schorb S, Rupp D, Adolph M, Gorkhover T, Andersson I, Hirsemann H, Potdevin G, Graafsma H, Nilsson B, Spence JC (2011) Femtosecond X-ray protein nanocrystallography. Nature 470:73–77PubMedCrossRefGoogle Scholar
  94. 94.
    Seibert MM, Ekeberg T, Maia FR, Svenda M, Andreasson J, Jönsson O, Odić D, Iwan B, Rocker A, Westphal D, Hantke M, DePonte DP, Barty A, Schulz J, Gumprecht L, Coppola N, Aquila A, Liang M, White TA, Martin A, Caleman C, Stern S, Abergel C, Seltzer V, Claverie JM, Bostedt C, Bozek JD, Boutet S, Miahnahri AA, Messerschmidt M, Krzywinski J, Williams G, Hodgson KO, Bogan MJ, Hampton CY, Sierra RG, Starodub D, Andersson I, Bajt S, Barthelmess M, Spence JC, Fromme P, Weierstall U, Kirian R, Hunter M, Doak RB, Marchesini S, Hau-Riege SP, Frank M, Shoeman RL, Lomb L, Epp SW, Hartmann R, Rolles D, Rudenko A, Schmidt C, Foucar L, Kimmel N, Holl P, Rudek B, Erk B, Hömke A, Reich C, Pietschner D, Weidenspointner G, Strüder L, Hauser G, Gorke H, Ullrich J, Schlichting I, Herrmann S, Schaller G, Schopper F, Soltau H, Kühnel KU, Andritschke R, Schröter CD, Krasniqi F, Bott M, Schorb S, Rupp D, Adolph M, Gorkhover T, Hirsemann H, Potdevin G, Graafsma H, Nilsson B, Chapman HN, Hajdu J (2011) Single mimivirus particles intercepted and imaged with an X-ray laser. Nature 470:78–81PubMedCrossRefGoogle Scholar
  95. 95.
    Lebbink MN, Geerts WJ, van der Krift TP, Bouwhuis M, Hertzberger LO, Verkleij AJ, Koster AJ (2007) Template matching as a tool for annotation of tomograms of stained biological structures. J Struct Biol 158:327–335PubMedCrossRefGoogle Scholar
  96. 96.
    Pintilie GD, Zhang J, Goddard TD, Chiu W, Gossard DC (2010) Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. J Struct Biol 170:427–438PubMedCrossRefGoogle Scholar
  97. 97.
    Liljeroos L, Huiskonen JT, Ora A, Susi P, Butcher SJ (2011) Electron cryotomography of measles virus reveals how matrix protein coats the ribonucleocapsid within intact virions. Proc Natl Acad Sci U S A 108:18085–18090PubMedCrossRefGoogle Scholar
  98. 98.
    Brandt F, Carlson LA, Hartl FU, Baumeister W, Grünewald K (2010) The three-dimensional organization of polyribosomes in intact human cells. Mol Cell 39:560–569PubMedCrossRefGoogle Scholar
  99. 99.
    Plitzko JM, Rigort A, Leis A (2009) Correlative cryo-light microscopy and cryo-electron tomography: from cellular territories to molecular landscapes. Curr Opin Biotechnol 20:83–89PubMedCrossRefGoogle Scholar
  100. 100.
    van Driel LF, Valentijn JA, Valentijn KM, Koning RI, Koster AJ (2009) Tools for correlative cryo-fluorescence microscopy and cryo-electron tomography applied to whole mitochondria in human endothelial cells. Eur J Cell Biol 88:669–684PubMedCrossRefGoogle Scholar
  101. 101.
    Kukulski W, Schorb M, Welsch S, Picco A, Kaksonen M, Briggs JA (2011) Correlated fluorescence and 3D electron microscopy with high sensitivity and spatial precision. J Cell Biol 192:111–119PubMedCrossRefGoogle Scholar
  102. 102.
    Jun S, Ke D, Debiec K, Zhao G, Meng X, Ambrose Z, Gibson GA, Watkins SC, Zhang P (2011) Direct visualization of HIV-1 with correlative live-cell microscopy and cryo-electron tomography. Structure 19:1573–1581PubMedCrossRefGoogle Scholar
  103. 103.
    Raines KS, Salha S, Sandberg RL, Jiang H, Rodriguez JA, Fahimian BP, Kapteyn HC, Du J, Miao J (2010) Three-dimensional structure determination from a single view. Nature 463:214–217PubMedCrossRefGoogle Scholar
  104. 104.
    Reich ES (2011) Three-dimensional technique on trial. Nature 480:303PubMedCrossRefGoogle Scholar
  105. 105.
    Hoppe W, Langer R, Frank J, Feltynowski A (1969) Image differentiation procedures in electron microscopy. Naturwissenschaften 56:267–272PubMedCrossRefGoogle Scholar
  106. 106.
    Maiden AM, Humphry MJ, Zhang F, Rodenburg JM (2011) Superresolution imaging via ptychography. J Opt Soc Am A Opt Image Sci Vis 28:604–612PubMedCrossRefGoogle Scholar
  107. 107.
    Dierolf M, Menzel A, Thibault P, Schneider P, Kewish CM, Wepf R, Bunk O, Pfeiffer F (2010) Ptychographic X-ray computed tomography at the nanoscale. Nature 467:436–439PubMedCrossRefGoogle Scholar
  108. 108.
    Rossmann MG (2012) Crystallography, evolution, and the structure of viruses. J Biol Chem 287:9552–9559PubMedCrossRefGoogle Scholar
  109. 109.
    McLellan JS, Pancera M, Carrico C, Gorman J, Julien JP, Khayat R, Louder R, Pejchal R, Sastry M, Dai K, O’Dell S, Patel N, Shahzad-ul-Hussan S, Yang Y, Zhang B, Zhou T, Zhu J, Boyington JC, Chuang GY, Diwanji D, Georgiev I, Kwon YD, Lee D, Louder MK, Moquin S, Schmidt SD, Yang ZY, Bonsignori M, Crump JA, Kapiga SH, Sam NE, Haynes BF, Burton DR, Koff WC, Walker LM, Phogat S, Wyatt R, Orwenyo J, Wang LX, Arthos J, Bewley CA, Mascola JR, Nabel GJ, Schief WR, Ward AB, Wilson IA, Kwong PD (2011) Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9. Nature 480:336–343PubMedCrossRefGoogle Scholar
  110. 110.
    Bahar MW, Graham SC, Stuart DI, Grimes JM (2011) Insights into the evolution of a complex virus from the crystal structure of vaccinia virus d13. Structure 19:1011–1020PubMedCrossRefGoogle Scholar
  111. 111.
    Coloma R, Valpuesta JM, Arranz R, Carrascosa JL, Ortin J, Martín-Benito J (2009) The structure of a biologically active influenza virus ribonucleoprotein complex. PLoS Pathog 5:e1000491PubMedCrossRefGoogle Scholar
  112. 112.
    Abrescia NG, Bamford DH, Grimes JM, Stuart DI (2012) Structure unifies the viral universe. Annu Rev Biochem 81:795–822PubMedCrossRefGoogle Scholar
  113. 113.
    Kaufmann B, Plevka P, Kuhn RJ, Rossmann MG (2010) Crystallization and preliminary X-ray diffraction analysis of West Nile virus. Acta Crystallogr Sect F Struct Biol Cryst Commun 66:558–562PubMedCrossRefGoogle Scholar
  114. 114.
    Kaufmann B, Nybakken GE, Chipman PR, Zhang W, Diamond MS, Fremont DH, Kuhn RJ, Rossmann MG (2006) West Nile virus in complex with the Fab fragment of a neutralizing monoclonal antibody. Proc Natl Acad Sci U S A 103:12400–12404PubMedCrossRefGoogle Scholar
  115. 115.
    Yu X, Qiao M, Atanasov I, Hu Z, Kato T, Liang TJ, Zhou ZH (2007) Cryo-electron microscopy and three-dimensional reconstructions of hepatitis C virus particles. Virology 367:126–134PubMedCrossRefGoogle Scholar
  116. 116.
    Badia-Martinez D, Peralta B, Andrés G, Guerra M, Gil-Carton D, Abrescia NG (2012) Three-dimensional visualization of forming Hepatitis C virus-like particles by electron-tomography. Virology 430:120–126PubMedCrossRefGoogle Scholar
  117. 117.
    Gastaminza P, Dryden KA, Boyd B, Wood MR, Law M, Yeager M, Chisari FV (2010) Ultrastructural and biophysical characterization of hepatitis C virus particles produced in cell culture. J Virol 84:10999–11009PubMedCrossRefGoogle Scholar
  118. 118.
    Owen RL, Axford D, Nettleship JE, Owens RJ, Robinson JI, Morgan AW, Doré AS, Lebon G, Tate CG, Fry EE, Ren J, Stuart DI, Evans G (2012) Outrunning free radicals in room-temperature macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 68:810–818PubMedCrossRefGoogle Scholar
  119. 119.
    Murata K, Liu X, Danev R, Jakana J, Schmid MF, King J, Nagayama K, Chiu W (2010) Zernike phase contrast cryo-electron microscopy and tomography for structure determination at nanometer and subnanometer resolutions. Structure 18:903–912PubMedCrossRefGoogle Scholar

Further Reading1

  1. Abeyrathne PD, Chami M, Pantelic RS, Goldie KN, Stahlberg H (2010) Preparation of 2D crystals of membrane proteins for high-resolution electron crystallography data collection. Methods Enzymol 481:25–43PubMedCrossRefGoogle Scholar
  2. Abrescia NG, Grimes JM, Fry EE, Ravantti JJ, Bamford DH, Stuart DI (2010) What does it take to make a virus: the concept of the viral “self”. In: Twarock R, Stockley PG (eds) Emerging topics in physical virology. Imperial College Press, London, pp 35–58CrossRefGoogle Scholar
  3. Derosier D (2010) 3D reconstruction from electron micrographs a personal account of its development. Methods Enzymol 481:1–24PubMedCrossRefGoogle Scholar
  4. Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL (2012) Outcome of the first electron microscopy validation task force meeting. Structure 20:205–214PubMedCrossRefGoogle Scholar
  5. Johnson JE (2008) Multi-disciplinary studies of viruses: the role of structure in shaping the questions and answers. J Struct Biol 163:246–253PubMedCrossRefGoogle Scholar
  6. Perutz MF, Rossmann MG, Cullis AF, Muirhead H, Will G, North AC (1960) Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-A. Resolution, obtained by X-ray analysis. Nature 185:416–422PubMedCrossRefGoogle Scholar
  7. Putnam CD, Hammel M, Hura GL, Tainer JA (2007) X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q Rev Biophys 40:191–285PubMedCrossRefGoogle Scholar
  8. Read RJ, Adams PD, Arendall WB III, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH (2011) A new generation of crystallographic validation tools for the protein data bank. Structure 19:1395–1412PubMedCrossRefGoogle Scholar
  9. Steven AC, Baumeister W (2008) The future is hybrid. J Struct Biol 163:186–195PubMedCrossRefGoogle Scholar
  10. Vellieux FM, Read RJ (1997) Noncrystallographic symmetry averaging in phase refinement and extension. Methods Enzymol 277:18–53PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Daniel Badia-Martinez
    • 1
  • Hanna M. Oksanen
    • 2
  • David I. Stuart
    • 3
    • 4
  • Nicola G. A. Abrescia
    • 1
    • 5
  1. 1.Structural Biology UnitCICbioGUNE, CIBERehd, Bizkaia Technology ParkDerioSpain
  2. 2.Institute of Biotechnology and Department of Biosciences, Viikki BiocenterUniversity of HelsinkiHelsinkiFinland
  3. 3.Division of Structural Biology, The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
  4. 4.Diamond Light Source LtdDidcotUK
  5. 5.Ikerbasque, Basque Foundation for ScienceBilbaoSpain

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