Skip to main content
SpringerLink
Log in

Reconstructing Virus Structures from Nanometer to Near-Atomic Resolutions with Cryo-Electron Microscopy and Tomography

  • Chapter
  • First Online:
Viral Molecular Machines

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 726))

Abstract

The past few decades have seen tremendous advances in single-particle electron ­cryo-microscopy (cryo-EM). The field has matured to the point that near-atomic resolution density maps can be generated for icosahedral viruses without the need for crystallization. In parallel, substantial progress has been made in determining the structures of nonicosahedrally arranged proteins in viruses by employing either single-particle cryo-EM or cryo-electron tomography (cryo-ET). Implicit in this course have been the availability of a new generation of electron cryo-microscopes and the development of the computational tools that are essential for generating these maps and models. This methodology has enabled structural biologists to analyze structures in increasing detail for virus particles that are in different morphogenetic states. Furthermore, electron imaging of frozen, hydrated cells, in the process of being infected by viruses, has also opened up a new avenue for studying virus structures “in situ”. Here we present the common techniques used to acquire and process cryo-EM and cryo-ET data and discuss their implications for structural virology both now and in the future.

Juan Chang, Xiangan Liu, Ryan H. Rochat and Matthew L. Baker contributed equally.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Abbreviations

1-D:

One dimension; one dimensional

2-D:

Two dimensions; two dimensional

3-D:

Three dimensions; three dimensional

CCD:

Charge-coupled device

Cryo-EM:

Electron cryo-microscopy

Cryo-ET:

Electron cryo-tomography

CT:

Computed tomography

CTF:

Contrast transfer function

EM:

Electron microscope; electron microscopy

EMDB:

Electron Microscopy Data Bank (http://www.emdatabank.org)

FSC:

Fourier shell correlation

FT:

Fourier transform

GUI:

Graphical user interface

SNR:

Signal-to-noise ratio

SSE:

Secondary structural elements

WPOA:

Weak phase object approximation

ZPC:

Zernike phase contrast

References

  • Abeysinghe SS, Baker ML, Chiu W, Ju T (2008) Segmentation-free skeletonization of grayscale volumes for shape understanding. In: IEEE international conference on shape modeling and applications, Stony Brook, NY

    Google Scholar 

  • Abeysinghe S, Baker ML, Chiu W, Ju T (2010) Semi-isometric registration of line features for flexible fitting of protein structures. Comput Graph Forum 29:2243–2252

    PubMed  Google Scholar 

  • Adrian M, Dubochet J, Lepault J, McDowall AW (1984) Cryo-electron microscopy of viruses. Nature 308:32–36

    PubMed  CAS  Google Scholar 

  • Agirrezabala X, Martín-Benito J, Castón JR, Miranda R, Valpuesta JM, Carrascosa JL (2005) Maturation of phage T7 involves structural modification of both shell and inner core components. EMBO J 24:3820–3829

    PubMed  CAS  Google Scholar 

  • Al-Amoudi A, Chang J-J, Leforestier Al, McDowall A, Salamin LM, Norlén LPO, Richter K, Blanc NS, Studer D, Dubochet J (2004) Cryo-electron microscopy of vitreous sections. EMBO J 23:3583–3588

    PubMed  CAS  Google Scholar 

  • Amat F, Moussavi F, Comolli LR, Elidan G, Downing KH, Horowitz M (2008) Markov random field based automatic image alignment for electron tomography. J Struct Biol 161:260–275

    PubMed  Google Scholar 

  • Baker D (2006) Prediction and design of macromolecular structures and interactions. Philos Trans R Soc Lond B Biol Sci 361:459–463

    PubMed  CAS  Google Scholar 

  • Baker TS, Cheng RH (1996) A model-based approach for determining orientations of biological macromolecules imaged by cryoelectron microscopy. J Struct Biol 116:120–130

    PubMed  CAS  Google Scholar 

  • Baker ML, Jiang W, Bowman BR, Zhou ZH, Quiocho FA, Rixon FJ, Chiu W (2003) Architecture of the herpes simplex virus major capsid protein derived from structural bioinformatics. J Mol Biol 331:447–456

    PubMed  CAS  Google Scholar 

  • Baker ML, Jiang W, Rixon FJ, Chiu W (2005) Common ancestry of herpesviruses and tailed DNA bacteriophages. J Virol 79:14967–14970

    PubMed  CAS  Google Scholar 

  • Baker ML, Jiang W, Wedemeyer WJ, Rixon FJ, Baker D, Chiu W (2006a) Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density. PLoS Comput Biol 2:e146

    PubMed  Google Scholar 

  • Baker ML, Yu Z, Chiu W, Bajaj C (2006b) Automated segmentation of molecular subunits in electron cryomicroscopy density maps. J Struct Biol 156:432–441

    PubMed  CAS  Google Scholar 

  • Baker ML, Ju T, Chiu W (2007) Identification of secondary structure elements in intermediate-resolution density maps. Structure 15:7–19

    PubMed  CAS  Google Scholar 

  • Baker ML, Baker MR, Hryc CF, Dimaio F (2010a) Analyses of subnanometer resolution cryo-EM density maps. Methods Enzymol 483:1–29

    PubMed  CAS  Google Scholar 

  • Baker ML, Zhang J, Ludtke SJ, Chiu W (2010b) Cryo-EM of macromolecular assemblies at near-atomic resolution. Nat Protoc 5:1697–1708

    PubMed  CAS  Google Scholar 

  • Baker ML, Abeysinghe SS, Schuh S, Coleman RA, Abrams A, Marsh MP, Hryc CF, Ruths T, Chiu W, Ju T (2011) Modeling protein structure at near atomic resolutions with Gorgon. J Struct Biol 174:360–373

    PubMed  CAS  Google Scholar 

  • Bammes BE, Jakana J, Schmid MF, Chiu W (2010) Radiation damage effects at four specimen temperatures from 4 to 100 K. J Struct Biol 169:331–341

    PubMed  CAS  Google Scholar 

  • Bartesaghi A, Sprechmann P, Liu J, Randall G, Sapiro G, Subramaniam S (2008) Classification and 3D averaging with missing wedge correction in biological electron tomography. J Struct Biol 162:436–450

    PubMed  CAS  Google Scholar 

  • Boersch H (1947) Über die Kontraste von Atomen im Elektronenmikroskop. Z Naturforsch 2a:615–633

    CAS  Google Scholar 

  • Bostina M, Levy H, Filman DJ, Hogle JM (2011) Poliovirus RNA is released from the capsid near a twofold symmetry axis. J Virol 85:776–783

    PubMed  CAS  Google Scholar 

  • Böttcher B, Wynne SA, Crowther RA (1997) Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature 386:88–91

    PubMed  Google Scholar 

  • Bradley P, Misura KM, Baker D (2005) Toward high-resolution de novo structure prediction for small proteins. Science 309:1868–1871

    PubMed  CAS  Google Scholar 

  • Brandt S, Heikkonen J, Engelhardt P (2001a) Automatic alignment of transmission electron microscope tilt series without fiducial markers. J Struct Biol 136:201–213

    PubMed  CAS  Google Scholar 

  • Brandt S, Heikkonen J, Engelhardt P (2001b) Multiphase method for automatic alignment of transmission electron microscope images using markers. J Struct Biol 133:10–22

    PubMed  CAS  Google Scholar 

  • Cambie R, Downing KH, Typke D, Glaeser RM, Jin J (2007) Design of a microfabricated, two-electrode phase-contrast element suitable for electron microscopy. Ultramicroscopy 107:329–339

    PubMed  CAS  Google Scholar 

  • Carragher B, Kisseberth N, Kriegman D, Milligan RA, Potter CS, Pulokas J, Reilein A (2000) Leginon: an automated system for acquisition of images from vitreous ice specimens. J Struct Biol 132:33–45

    PubMed  CAS  Google Scholar 

  • Castano-Diez D, Al-Amoudi A, Glynn AM, Seybert A, Frangakis AS (2007) Fiducial-less alignment of cryo-sections. J Struct Biol 159:413–423

    PubMed  Google Scholar 

  • Castano-Diez D, Scheffer M, Al-Amoudi A, Frangakis AS (2010) Alignator: a GPU powered software package for robust fiducial-less alignment of cryo tilt-series. J Struct Biol 170:117–126

    PubMed  CAS  Google Scholar 

  • Chang J, Weigele P, King J, Chiu W, Jiang W (2006) Cryo-EM asymmetric reconstruction of bacteriophage P22 reveals organization of its DNA packaging and infecting machinery. Structure 14:1073–1082

    PubMed  CAS  Google Scholar 

  • Chang JT, Schmid MF, Haase-Pettingell C, Weigele PR, King JA, Chiu W (2010) Visualizing the structural changes of bacteriophage epsilon15 and its Salmonella host during infection. J Mol Biol 402:731–740

    PubMed  CAS  Google Scholar 

  • Chen B, Vogan EM, Gong H, Skehel JJ, Wiley DC, Harrison SC (2005) Structure of an unliganded simian immunodeficiency virus gp120 core. Nature 433:834–841

    PubMed  CAS  Google Scholar 

  • Chen D-H, Luke K, Zhang J, Chiu W, Wittung-Stafshede P (2008) Location and flexibility of the unique C-terminal tail of Aquifex aeolicus co-chaperonin protein 10 as derived by cryo-electron microscopy and biophysical techniques. J Mol Biol 381:707–717

    PubMed  CAS  Google Scholar 

  • Chen JZ, Settembre EC, Aoki ST, Zhang X, Bellamy AR, Dormitzer PR, Harrison SC, Grigorieff N (2009) Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM. Proc Natl Acad Sci USA 106:10644–10648

    PubMed  CAS  Google Scholar 

  • Chen D-H, Baker ML, Hryc CF, DiMaio F, Jakana J, Wu W, Dougherty M, Haase-Pettingell C, Schmid MF, Jiang W et al (2011) Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Proc Natl Acad Sci USA 108:1355–1360

    PubMed  CAS  Google Scholar 

  • Cheng L, Sun J, Zhang K, Mou Z, Huang X, Ji G, Sun F, Zhang J, Zhu P (2011) Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping. Proc Natl Acad Sci USA 108:1373–1378

    PubMed  CAS  Google Scholar 

  • Chiu W (1986) Electron microscopy of frozen, hydrated biological specimens. Ann Rev Biophys Biophys Chem 15:237–257

    CAS  Google Scholar 

  • Chiu W, Glaeser RM (1977) Factors affecting high resolution fixed-beam transmission electron microscopy. Ultramicroscopy 2:207–217

    PubMed  CAS  Google Scholar 

  • Chiu W, Baker ML, Jiang W, Dougherty M, Schmid MF (2005) Electron cryomicroscopy of biological machines at subnanometer resolution. Structure 13:363–372

    PubMed  CAS  Google Scholar 

  • Comolli LR, Downing KH (2005) Dose tolerance at helium and nitrogen temperatures for whole cell electron tomography. J Struct Biol 152:149–156

    PubMed  CAS  Google Scholar 

  • Cong Y, Ludtke SJ (2010) Single particle analysis at high resolution. Methods Enzymol 482:211–235

    PubMed  CAS  Google Scholar 

  • Cong Y, Kovacs JA, Wriggers W (2003) 2D fast rotational matching for image processing of biophysical data. J Struct Biol 144:51–60

    PubMed  Google Scholar 

  • Conway JF, Cheng N, Zlotnick A, Wingfield PT, Stahl SJ, Steven AC (1997) Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy. Nature 386:91–94

    PubMed  CAS  Google Scholar 

  • Crowther RA (1971) Procedures for three-dimensional reconstruction of spherical viruses by Fourier synthesis from electron micrographs. Philos Trans R Soc Lond B Biol Sci 261:221–230

    PubMed  CAS  Google Scholar 

  • Crowther RA, Amos LA, Finch JT, De Rosier DJ, Klug A (1970a) Three dimensional reconstructions of spherical viruses by Fourier synthesis from electron micrographs. Nature 226:421–425

    PubMed  CAS  Google Scholar 

  • Crowther RA, DeRosier DJ, Klug A (1970b) The reconstruction of a three-dimensional structure from projections and its application to electron microscopy. Proc R Soc Lond A 317:319–340

    Google Scholar 

  • Cyrklaff M, Linaroudis A, Boicu M, Chlanda P, Baumeister W, Griffiths G, Krijnse-Locker J (2007) Whole cell cryo-electron tomography reveals distinct disassembly intermediates of vaccinia virus. PLoS One 2:e420

    Google Scholar 

  • Danev R, Nagayama K (2001) Transmission electron microscopy with Zernike phase plate. Ultramicroscopy 88:243–252

    PubMed  CAS  Google Scholar 

  • Danev R, Nagayama K (2008) Single particle analysis based on Zernike phase contrast transmission electron microscopy. J Struct Biol 161:211–218

    PubMed  CAS  Google Scholar 

  • Deptuch G, Besson A, Rehak P, Szelezniak M, Wall J, Winter M, Zhu Y (2007) Direct electron imaging in electron microscopy with monolithic active pixel sensors. Ultramicroscopy 107:674–684

    PubMed  CAS  Google Scholar 

  • DeRosier DJ (2000) Correction of high-resolution data for curvature of the Ewald sphere. Ultramicroscopy 81:83–98

    PubMed  CAS  Google Scholar 

  • DeRosier DL, Klug A (1968) Reconstruction of three-dimensional structures from electron micrographs. Nature 217:130–134

    Google Scholar 

  • DiMaio F, Tyka MD, Baker ML, Chiu W, Baker D (2009) Refinement of protein structures into low-resolution density maps using rosetta. J Mol Biol 392:181–190

    PubMed  CAS  Google Scholar 

  • DiMaio F, Terwilliger TC, Read RJ, Wlodawer A, Oberdorfer G, Wagner U, Valkov E, Alon A, Fass D, Axelrod HL et al (2011) Improved molecular replacement by density- and energy-guided protein structure optimization. Nature 473(7348):540–543

    PubMed  CAS  Google Scholar 

  • Dubochet J, Adrian M, Chang JJ, Homo JC, Lepault J, McDowall AW, Schultz P (1988) Cryo-electron microscopy of vitrified specimens. Q Rev Biophys 21:129–228

    PubMed  CAS  Google Scholar 

  • Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126–2132

    PubMed  Google Scholar 

  • Erickson HP, Klug A (1971) Measurement and compensation of defocusing and aberrations by Fourier processing of electron micrographs. Phil Trans R Soc Lond B 261:105–118

    Google Scholar 

  • Fernandez JJ, Li S, Crowther RA (2006) CTF determination and correction in electron cryotomography. Ultramicroscopy 106:587–596

    PubMed  CAS  Google Scholar 

  • Fernandez JJ, Luque D, Caston JR, Carrascosa JL (2008) Sharpening high resolution information in single particle electron cryomicroscopy. J Struct Biol 164:170–175

    PubMed  CAS  Google Scholar 

  • Forster F, Pruggnaller S, Seybert A, Frangakis AS (2008) Classification of cryo-electron sub-tomograms using constrained correlation. J Struct Biol 161:276–286

    PubMed  Google Scholar 

  • Förster F, Medalia O, Zauberman N, Baumeister W, Fass D (2005) Retrovirus envelope protein complex structure in situ studied by cryo-electron tomography. Proc Natl Acad Sci USA 102:4729–4734

    PubMed  Google Scholar 

  • Fu C-Y, Wang K, Gan L, Lanman J, Khayat R, Young MJ, Jensen GJ, Doerschuk PC, Johnson JE (2010) In vivo assembly of an archaeal virus studied with whole-cell electron cryotomography. Structure 18:1579–1586

    PubMed  CAS  Google Scholar 

  • Fuller SD, Butcher SJ, Cheng RH, Baker TS (1996) Three-dimensional reconstruction of icosahedral particles – the uncommon line. J Struct Biol 116:48–55

    PubMed  CAS  Google Scholar 

  • Gilbert PF (1972) The reconstruction of a three-dimensional structure from projections and its application to electron microscopy. II. Direct methods. Proc R Soc Lond B Biol Sci 182:89–102

    PubMed  CAS  Google Scholar 

  • Glaeser RM, Downing KH, DeRosier D, Chiu W, Frank J (2007) Electron crystallography of biological macromolecules. Oxford University Press, New York

    Google Scholar 

  • Grigorieff N, Harrison SC (2011) Near-atomic resolution reconstructions of icosahedral viruses from electron cryo-microscopy. Curr Opin Struct Biol 21:265–273

    PubMed  CAS  Google Scholar 

  • Hendrix RW (1978) Symmetry mismatch and DNA packaging in large bacteriophages. Proc Natl Acad Sci USA 75:4779–4783

    PubMed  CAS  Google Scholar 

  • Heymann JB, Cardone G, Winkler DC, Steven AC (2008) Computational resources for cryo-electron tomography in Bsoft. J Struct Biol 161:232–242

    PubMed  Google Scholar 

  • Ho MH, Jap BK, Glaeser RM (1988) Validity domain of the weak-phase-object approximation for electron diffraction of thin protein crystals. Acta Crystallogr A 44(Pt 6):878–884

    PubMed  Google Scholar 

  • Hoenger A, Bouchet-Marquis C (2011) Cellular tomography. Adv Protein Chem Struct Biol 82:67–90

    PubMed  CAS  Google Scholar 

  • Hryc CF, Chen DH, Chiu W (2011) Near-atomic-resolution cryo-EM for molecular virology. Curr Opin Virol 1(2):110–117

    PubMed  CAS  Google Scholar 

  • Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33–38, 27–38

    Google Scholar 

  • Iancu CV, Wright ER, Heymann JB, Jensen GJ (2006) A comparison of liquid nitrogen and liquid helium as cryogens for electron cryotomography. J Struct Biol 153:231–240

    PubMed  CAS  Google Scholar 

  • Jiang W, Chiu W (2007) Cryoelectron microscopy of icosahedral virus particles. Methods Mol Biol 369:345–363

    PubMed  CAS  Google Scholar 

  • Jiang W, Baker ML, Ludtke SJ, Chiu W (2001a) Bridging the information gap: computational tools for intermediate resolution structure interpretation. J Mol Biol 308:1033–1044

    PubMed  CAS  Google Scholar 

  • Jiang W, Li Z, Zhang Z, Booth CR, Baker ML, Chiu W (2001b) Semi-automated icosahedral particle reconstruction at sub-nanometer resolution. J Struct Biol 136:214–225

    PubMed  CAS  Google Scholar 

  • Jiang W, Chang J, Jakana J, Weigele P, King J, Chiu W (2006) Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus. Nature 439:612–616

    PubMed  CAS  Google Scholar 

  • 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 451:1130–1134

    PubMed  CAS  Google Scholar 

  • Johnson, J.E. & Fisher, AJ (1994) Principles of virus structure. In Encyclopedia of Virology (Webster, R.G. & Granoff, A., eds.), London, Academic Press, 1573–1586

    Google Scholar 

  • Jones TA, Zou JY, Cowan SW, Kjeldgaard M (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 47(Pt 2):110–119

    PubMed  Google Scholar 

  • Joyeux L, Penczek PA (2002) Efficiency of 2D alignment methods. Ultramicroscopy 92:33–46

    PubMed  CAS  Google Scholar 

  • Ju T, Baker ML, Chiu W (2007) Computing a family of skeletons of volumetric models for shape description. Comput Aided Des 39:352–360

    PubMed  Google Scholar 

  • Kleywegt GJ, Jones TA (1997) Detecting folding motifs and similarities in protein structures. Methods Enzymol 277:525–545

    PubMed  CAS  Google Scholar 

  • Kong Y, Ma J (2003) A structural-informatics approach for mining beta-sheets: locating sheets in intermediate-­resolution density maps. J Mol Biol 332:399–413

    PubMed  CAS  Google Scholar 

  • Kong Y, Zhang X, Baker TS, Ma J (2004) A structural-informatics approach for tracing beta-sheets: building pseudo-C(alpha) traces for beta-strands in intermediate-resolution density maps. J Mol Biol 339:117–130

    PubMed  CAS  Google Scholar 

  • Kremer JR, Mastronarde DN, McIntosh JR (1996) Computer visualization of three-dimensional image data using IMOD. J Struct Biol 116:71–76

    PubMed  CAS  Google Scholar 

  • Lakshminarayanan AV, Lent A (1979) Methods of least squares and SIRT in reconstruction. J Theor Biol 76:267–295

    PubMed  CAS  Google Scholar 

  • Lander GC, Tang L, Casjens SR, Gilcrease EB, Prevelige P, Poliakov A, Potter CS, Carragher B, Johnson JE (2006) The structure of an infectious P22 virion shows the signal for headful DNA packaging. Science 312:1791–1795

    PubMed  CAS  Google Scholar 

  • Lawrence A, Bouwer JC, Perkins G, Ellisman MH (2006) Transform-based backprojection for volume reconstruction of large format electron microscope tilt series. J Struct Biol 154:144–167

    PubMed  CAS  Google Scholar 

  • Leiman PG, Battisti AJ, Bowman VD, Stummeyer K, Muhlenhoff M, Gerardy-Schahn R, Scholl D, Molineux IJ (2007) The structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities. J Mol Biol 371:836–849

    PubMed  CAS  Google Scholar 

  • Leiman PG, Arisaka F, van Raaij MJ, Kostyuchenko VA, Aksyuk AA, Kanamaru S, Rossmann MG (2010) Morphogenesis of the T4 tail and tail fibers. Virol J 7:355

    PubMed  CAS  Google Scholar 

  • Leong PA, Yu X, Zhou ZH, Jensen GJ (2010) Correcting for the Ewald sphere in high-resolution single-particle reconstructions. Methods Enzymol 482:369–380

    PubMed  Google Scholar 

  • Liang Y, Ke EY, Zhou ZH (2002) IMIRS: a high-resolution 3D reconstruction package integrated with a relational image database. J Struct Biol 137:292–304

    PubMed  CAS  Google Scholar 

  • Liu Y, Penczek PA, McEwen BF, Frank J (1995) A marker-free alignment method for electron tomography. Ultramicroscopy 58:393–402

    PubMed  CAS  Google Scholar 

  • Liu X, Jiang W, Jakana J, Chiu W (2007) Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. J Struct Biol 160:11–27

    PubMed  CAS  Google Scholar 

  • Liu H, Cheng L, Zeng S, Cai C, Zhou ZH, Yang Q (2008a) Symmetry-adapted spherical harmonics method for high-resolution 3D single-particle reconstructions. J Struct Biol 161:64–73

    PubMed  CAS  Google Scholar 

  • Liu J, Bartesaghi A, Borgnia MJ, Sapiro G, Subramaniam S (2008b) Molecular architecture of native HIV-1 gp120 trimers. Nature 455:109–113

    PubMed  CAS  Google Scholar 

  • Liu H, Jin L, Koh SB, Atanasov I, Schein S, Wu L, Zhou ZH (2010a) Atomic structure of human adenovirus by cryo-EM reveals interactions among protein networks. Science 329:1038–1043

    PubMed  CAS  Google Scholar 

  • Liu X, Rochat RH, Chiu W (2010b) Reconstructing cyano-bacteriophage P-SSP7 structure without imposing symmetry. Nat Protoc. doi:10.1038/nprot.2010.1096

  • Liu X, Zhang Q, Murata K, Baker ML, Sullivan MB, Fu C, Dougherty MT, Schmid MF, Osburne MS, Chisholm SW, Chiu W (2010c) Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus. Nat Struct Mol Biol 17:830–836

    PubMed  CAS  Google Scholar 

  • Ludtke SJ, Baldwin PR, Chiu W (1999) EMAN: semiautomated software for high-resolution single-particle reconstructions. J Struct Biol 128:82–97

    PubMed  CAS  Google Scholar 

  • Ludtke SJ, Baker ML, Chen DH, Song JL, Chuang DT, Chiu W (2008) De Novo backbone trace of GroEL from single particle electron cryomicroscopy. Structure 16:441–448

    PubMed  CAS  Google Scholar 

  • Ludtke SJ, Tran TP, Ngo QT, Moiseenkova-Bell VY, Chiu W, Serysheva I (2011) Flexible architecture of IP3R1 by cryo-EM. Structure 19(8):1192–1199

    PubMed  CAS  Google Scholar 

  • Marabini R, Herman GT, Carazo JM (1998) 3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs). Ultramicroscopy 72:53–65

    PubMed  CAS  Google Scholar 

  • Mastronarde DN (1997) Dual-axis tomography: an approach with alignment methods that preserve resolution. J Struct Biol 120:343–352

    PubMed  CAS  Google Scholar 

  • McDowall AW, Chang JJ, Freeman R, Lepault J, Walter CA, Dubochet J (1983) Electron microscopy of frozen hydrated sections of vitreous ice and vitrified biological samples. J Microsc 131:1–9

    PubMed  CAS  Google Scholar 

  • McMullan G, Chen S, Henderson R, Faruqi AR (2009) Detective quantum efficiency of electron area detectors in electron microscopy. Ultramicroscopy 109:1126–1143

    PubMed  CAS  Google Scholar 

  • Milazzo AC, Leblanc P, Duttweiler F, Jin L, Bouwer JC, Peltier S, Ellisman M, Bieser F, Matis HS, Wieman H et al (2005) Active pixel sensor array as a detector for electron microscopy. Ultramicroscopy 104:152–159

    PubMed  CAS  Google Scholar 

  • Milazzo AC, Moldovan G, Lanman J, Jin L, Bouwer JC, Klienfelder S, Peltier ST, Ellisman MH, Kirkland AI, Xuong NH (2010) Characterization of a direct detection device imaging camera for transmission electron microscopy. Ultramicroscopy 110:744–747

    PubMed  Google Scholar 

  • Mindell JA, Grigorieff N (2003) Accurate determination of local defocus and specimen tilt in electron microscopy. J Struct Biol 142:334–347

    PubMed  Google Scholar 

  • Miyazaki Y, Irobalieva RN, Tolbert BS, Smalls-Mantey A, Iyalla K, Loeliger K, D’Souza V, Khant H, Schmid MF, Garcia EL et al (2010) Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography. J Mol Biol 404:751–772

    PubMed  CAS  Google Scholar 

  • Mizuguchi K, Go N (1995) Comparison of spatial arrangements of secondary structural elements in proteins. Protein Eng 8:353–362

    PubMed  CAS  Google Scholar 

  • 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 18:903–912

    PubMed  CAS  Google Scholar 

  • Nakamura N, Shimizu Y, Shinkawa T, Nakata M, Bammes B, Zhang J, Chiu W (2010) Automated specimen search in cryo-TEM observation with DIFF-defocus imaging. J Electron Microsc 59:299–310

    Google Scholar 

  • Nicastro D, Schwartz C, Pierson J, Gaudette R, Porter ME, McIntosh JR (2006) The molecular architecture of axonemes revealed by cryoelectron tomography. Science 313:944–948

    PubMed  CAS  Google Scholar 

  • Nickell S, Förster 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 149:227–234

    PubMed  Google Scholar 

  • Penczek PA, Yang C, Frank J, Spahn CM (2006) Estimation of variance in single-particle reconstruction using the bootstrap technique. J Struct Biol 154:168–183

    PubMed  CAS  Google Scholar 

  • Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera – a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612

    PubMed  CAS  Google Scholar 

  • 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 170:427–438

    PubMed  CAS  Google Scholar 

  • Potter CS, Chu H, Frey B, Green C, Kisseberth N, Madden TJ, Miller KL, Nahrstedt K, Pulokas J, Reilein A et al (1999) Leginon: a system for fully automated acquisition of 1000 electron micrographs a day. Ultramicroscopy 77:153–161

    PubMed  CAS  Google Scholar 

  • Reddy VS, Natchiar SK, Stewart PL, Nemerow GR (2010) Crystal structure of human adenovirus at 3.5 A resolution. Science 329:1071–1075

    PubMed  CAS  Google Scholar 

  • Rochat RH, Liu X, Murata K, Nagayama K, Rixon FJ, Chiu W (2011) Seeing the portal in herpes simplex virus type 1 B capsids. J Virol 85:1871–1874

    PubMed  CAS  Google Scholar 

  • Roseman AM (2000) Docking structures of domains into maps from cryo-electron microscopy using local correlation. Acta Crystallogr D Biol Crystallogr 56:1332–1340

    PubMed  CAS  Google Scholar 

  • Rosenthal PB, Henderson R (2003) Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J Mol Biol 333:721–745

    PubMed  CAS  Google Scholar 

  • Rossmann MG (2000) Fitting atomic models into electron-microscopy maps. Acta Crystallogr D Biol Crystallogr 56:1341–1349

    PubMed  CAS  Google Scholar 

  • Rossmann MG, Morais MC, Leiman PG, Zhang W (2005) Combining X-ray crystallography and electron microscopy. Structure 13:355–362

    PubMed  CAS  Google Scholar 

  • Rusu M, Birmanns S, Wriggers W (2008) Biomolecular pleiomorphism probed by spatial interpolation of coarse models. Bioinformatics 24:2460–2466

    PubMed  CAS  Google Scholar 

  • Saad A, Ludtke SJ, Jakana J, Rixon FJ, Tsuruta H, Chiu W (2001) Fourier amplitude decay of electron cryomicroscopic images of single particles and effects on structure determination. J Struct Biol 133:32–42

    PubMed  CAS  Google Scholar 

  • Saxton WO, Baumeister W, Hahn M (1984) Three-dimensional reconstruction of imperfect two-dimensional crystals. Ultramicroscopy 13:57–70

    PubMed  CAS  Google Scholar 

  • Schmid MF (2011) Single-particle electron cryotomography (cryoET). Adv Protein Chem Struct Biol 82:37–65

    PubMed  CAS  Google Scholar 

  • Schmid MF, Booth CR (2008) Methods for aligning and for averaging 3D volumes with missing data. J Struct Biol 161:243–248

    PubMed  Google Scholar 

  • Schmid MF, Prasad BV, Chiu W (1994) Structural studies of viruses by electron cryomicroscopy. Arch Virol Suppl 9:523–529

    PubMed  CAS  Google Scholar 

  • Schmid MF, Sherman MB, Matsudaira P, Tsuruta H, Chiu W (1999) Scaling structure factor amplitudes in electron cryomicroscopy using X-Ray solution scattering. J Struct Biol 128:51–57

    PubMed  CAS  Google Scholar 

  • Schmid MF, Paredes AM, Khant HA, Soyer F, Aldrich HC, Chiu W, Shively JM (2006) Structure of Halothiobacillus neapolitanus carboxysomes by cryo-electron tomography. J Mol Biol 364:526–535

    PubMed  CAS  Google Scholar 

  • Schröder GF, Brunger AT, Levitt M (2007) Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution. Structure 15:1630–1641

    PubMed  Google Scholar 

  • Settembre EC, Chen JZ, Dormitzer PR, Grigorieff N, Harrison SC (2011) Atomic model of an infectious rotavirus particle. EMBO J 30:408–416

    PubMed  CAS  Google Scholar 

  • Shaikh TR, Gao H, Baxter WT, Asturias FJ, Boisset N, Leith A, Frank J (2008) SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nat Protoc 3:1941–1974

    PubMed  CAS  Google Scholar 

  • Siebert X, Navaza J (2009) UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions. Acta Crystallogr D Biol Crystallogr 65:651–658

    PubMed  Google Scholar 

  • Sorzano CO, Messaoudi C, Eibauer M, Bilbao-Castro JR, Hegerl R, Nickell S, Marco S, Carazo JM (2009) Marker-free image registration of electron tomography tilt-series. BMC Bioinformatics 10:124

    PubMed  Google Scholar 

  • Stagg SM, Lander GC, Pulokas J, Fellmann D, Cheng A, Quispe JD, Mallick SP, Avila RM, Carragher B, Potter CS (2006) Automated cryoEM data acquisition and analysis of 284742 particles of GroEL. J Struct Biol 155:470–481

    PubMed  CAS  Google Scholar 

  • Stark H, Woods J, Paul I, Hingorania R (1981) Direct Fourier reconstruction in computer tomography. IEEE Trans Acoust Speech Signal Process 29:237–245

    Google Scholar 

  • Suhre K, Navaza J, Sanejouand YH (2006) NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps. Acta Crystallogr D Biol Crystallogr 62:1098–1100

    PubMed  Google Scholar 

  • Tama F, Miyashita O, Brooks CL (2004) Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J Struct Biol 147:315–326

    PubMed  CAS  Google Scholar 

  • Tan RKZ, Devkota B, Harvey SC (2008) YUP.SCX: coaxing atomic models into medium resolution electron density maps. J Struct Biol 163:163–174

    PubMed  CAS  Google Scholar 

  • Tang G, Peng L, Baldwin PR, Mann DS, Jiang W, Rees I, Ludtke SJ (2007) EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol 157:38–46

    PubMed  CAS  Google Scholar 

  • Tang J, Olson N, Jardine PJ, Grimes S, Anderson DL, Baker TS (2008) DNA poised for release in bacteriophage phi29. Structure 16:935–943

    PubMed  CAS  Google Scholar 

  • Taylor KA, Glaeser RM (1974) Electron diffraction of frozen, hydrated protein crystals. Science 186:1036–1037

    PubMed  CAS  Google Scholar 

  • Taylor KA, Glaeser RM (1976) Electron microscopy of frozen hydrated biological specimens. J Ultrastruct Res 55:448–456

    PubMed  CAS  Google Scholar 

  • Thon F (1971) Phase contrast electron microscopy. In: Valdre U (ed) Electron microscopy in material sciences. New York, Academic, pp 571–625

    Google Scholar 

  • Topf M, Sali A (2005) Combining electron microscopy and comparative protein structure modeling. Curr Opin Struct Biol 15:578–585

    PubMed  CAS  Google Scholar 

  • Topf M, Baker ML, John B, Chiu W, Sali A (2005) Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. J Struct Biol 149:191–203

    PubMed  CAS  Google Scholar 

  • Topf M, Baker ML, Marti-Renom MA, Chiu W, Sali A (2006) Refinement of protein structures by iterative comparative modeling and cryoEM density fitting. J Mol Biol 357:1655–1668

    PubMed  CAS  Google Scholar 

  • Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A (2008) Protein structure fitting and refinement guided by cryo-EM density. Structure 16:295–307

    PubMed  CAS  Google Scholar 

  • Trabuco LG, Villa E, Schreiner E, Harrison CB, Schulten K (2009) Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography. Methods 49:174–180

    PubMed  CAS  Google Scholar 

  • Trabuco LG, Schreiner E, Eargle J, Cornish P, Ha T, Luthey-Schulten Z, Schulten K (2010) The role of L1 stalk-tRNA interaction in the ribosome elongation cycle. J Mol Biol 402:741–760

    PubMed  CAS  Google Scholar 

  • Unwin PN, Henderson R (1975) Molecular structure determination by electron microscopy of unstained crystalline specimens. J Mol Biol 94:425–440

    PubMed  CAS  Google Scholar 

  • Volkmann N (2002) A novel three-dimensional variant of the watershed transform for segmentation of electron density maps. J Struct Biol 138:123–129

    PubMed  CAS  Google Scholar 

  • Volkmann N, Hanein D (1999) Quantitative fitting of atomic models into observed densities derived by electron microscopy. J Struct Biol 125:176–184

    PubMed  CAS  Google Scholar 

  • Walz J, Typke D, Nitsch M, Koster AJ, Hegerl R, Baumeister W (1997) Electron tomography of single ice-embedded macromolecules: three-dimensional alignment and classification. J Struct Biol 120:387–395

    PubMed  CAS  Google Scholar 

  • Winkler H (2007) 3D reconstruction and processing of volumetric data in cryo-electron tomography. J Struct Biol 157:126–137

    PubMed  CAS  Google Scholar 

  • Winkler H, Taylor KA (2003) Focus gradient correction applied to tilt series image data used in electron tomography. J Struct Biol 143:24–32

    PubMed  Google Scholar 

  • Winkler H, Taylor KA (2006) Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography. Ultramicroscopy 106:240–254

    PubMed  CAS  Google Scholar 

  • Wolf M, Garcea RL, Grigorieff N, Harrison SC (2010) Subunit interactions in bovine papillomavirus. Proc Natl Acad Sci USA 107:6298–6303

    PubMed  CAS  Google Scholar 

  • Wriggers W, Milligan RA, McCammon JA (1999) Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. J Struct Biol 125:185–195

    PubMed  CAS  Google Scholar 

  • Wright ER, Iancu CV, Tivol WF, Jensen GJ (2006) Observations on the behavior of vitreous ice at approximately 82 and approximately 12 K. J Struct Biol 153:241–252

    PubMed  Google Scholar 

  • Xiong Q, Morphew MK, Schwartz CL, Hoenger AH, Mastronarde DN (2009) CTF determination and correction for low dose tomographic tilt series. J Struct Biol 168:378–387

    PubMed  Google Scholar 

  • Yan X, Sinkovits RS, Baker TS (2007) AUTO3DEM – an automated and high throughput program for image reconstruction of icosahedral particles. J Struct Biol 157:73–82

    PubMed  CAS  Google Scholar 

  • Yu X, Jin L, Zhou ZH (2008) 3.88 A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy. Nature 453:415–419

    PubMed  CAS  Google Scholar 

  • Zanetti G, Briggs JA, Grunewald K, Sattentau QJ, Fuller SD (2006) Cryo-electron tomographic structure of an immunodeficiency virus envelope complex in situ. PLoS Pathog 2:e83

    PubMed  Google Scholar 

  • Zhang X, Settembre E, Xu C, Dormitzer PR, Bellamy R, Harrison SC, Grigorieff N (2008) Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction. Proc Natl Acad Sci USA 105:1867–1872

    PubMed  CAS  Google Scholar 

  • Zhang J, Nakamura N, Shimizu Y, Liang N, Liu X, Jakana J, Marsh MP, Booth CR, Shinkawa T, Nakata M, Chiu W (2009) JADAS: a customizable automated data acquisition system and its application to ice-embedded single particles. J Struct Biol 165:1–9

    PubMed  CAS  Google Scholar 

  • Zhang J, Baker ML, Schröder GF, Douglas NR, Reissmann S, Jakana J, Dougherty M, Fu CJ, Levitt M, Ludtke SJ et al (2010a) Mechanism of folding chamber closure in a group II chaperonin. Nature 463:379–383

    PubMed  CAS  Google Scholar 

  • Zhang X, Jin L, Fang Q, Hui WH, Zhou ZH (2010b) 3.3 A cryo-EM structure of a nonenveloped virus reveals a priming mechanism for cell entry. Cell 141:472–482

    PubMed  CAS  Google Scholar 

  • Zheng SQ, Keszthelyi B, Branlund E, Lyle JM, Braunfeld MB, Sedat JW, Agard DA (2007) UCSF tomography: an integrated software suite for real-time electron microscopic tomographic data collection, alignment, and reconstruction. J Struct Biol 157:138–147

    PubMed  CAS  Google Scholar 

  • Zhou ZH (2011) Atomic resolution cryo electron microscopy of macromolecular complexes. Adv Protein Chem Struct Biol 82:1–35

    PubMed  CAS  Google Scholar 

  • Zhou ZH, Chiu W (2003) Determination of icosahedral virus structures by electron cryomicroscopy at subnanometer resolution. Adv Protein Chem 64:93–124

    PubMed  CAS  Google Scholar 

  • Zhou ZH, Chiu W, Haskell K, Spears H Jr, Jakana J, Rixon FJ, Scott LR (1998) Refinement of herpesvirus B-capsid structure on parallel supercomputers. Biophys J 74:576–588

    PubMed  CAS  Google Scholar 

  • Zhou ZH, Dougherty M, Jakana J, He J, Rixon FJ, Chiu W (2000) Seeing the herpesvirus capsid at 8.5 Å. Science 288:877–880

    PubMed  CAS  Google Scholar 

  • Zhou ZH, Baker ML, Jiang W, Dougherty M, Jakana J, Dong G, Lu G, Chiu W (2001) Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus. Nat Struct Biol 8:868–873

    PubMed  CAS  Google Scholar 

  • Zhu J, Cheng L, Fang Q, Zhou ZH, Honig B (2010) Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement. J Mol Biol 397:835–851

    PubMed  CAS  Google Scholar 

Download references

Acknowledgments

JC, XL, RHR and MLB contributed equally to this work. This work has been supported by grants from NIH (P41RR002250, R01AI0175208, and R01GM079429) and Robert Welch Foundation (Q1242). RHR is supported by the NIH training grants (GM07330 through the MSTP, T15LM007093 through the Gulf Coast Consortia). We thank Dr. Frazer Rixon for assistance with manuscript preparation.

Author information

Authors and Affiliations

  1. National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA

    Juan Chang, Xiangan Liu, Ryan H. Rochat, Matthew L. Baker & Wah Chiu

  2. Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA

    Ryan H. Rochat & Wah Chiu

Authors
  1. Juan Chang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xiangan Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ryan H. Rochat
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Matthew L. Baker
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Wah Chiu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Wah Chiu .

Editor information

Editors and Affiliations

  1. Dept. Biological Sciences, Purdue University, W. State St. 915, West Lafayette, 47907-2054, Indiana, USA

    Michael G. Rossmann

  2. Dept. Biology, Catholic University of America, Washington, 20064, District of Columbia, USA

    Venigalla B. Rao

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Chang, J., Liu, X., Rochat, R.H., Baker, M.L., Chiu, W. (2012). Reconstructing Virus Structures from Nanometer to Near-Atomic Resolutions with Cryo-Electron Microscopy and Tomography. In: Rossmann, M., Rao, V. (eds) Viral Molecular Machines. Advances in Experimental Medicine and Biology, vol 726. Springer, Boston, MA. https://doi.org/10.1007/978-1-4614-0980-9_4

Download citation

Publish with us

Policies and ethics

Search

Navigation