Structure determination of a human virus by the combination of cryo-EM and X-ray crystallography

Zheng Liu; Tom S. Y. Guu; Jianhao Cao; Yinyin Li; Lingpeng Cheng; Yizhi Jane Tao; Jingqiang Zhang

doi:10.1007/s41048-016-0027-2

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Article Navigation > Biophysics Reports > 2016 > 2(2-4): 55-68

Zheng Liu, Tom S. Y. Guu, Jianhao Cao, Yinyin Li, Lingpeng Cheng, Yizhi Jane Tao, Jingqiang Zhang. Structure determination of a human virus by the combination of cryo-EM and X-ray crystallography. Biophysics Reports, 2016, 2(2-4): 55-68. doi: 10.1007/s41048-016-0027-2

Citation:

Zheng Liu, Tom S. Y. Guu, Jianhao Cao, Yinyin Li, Lingpeng Cheng, Yizhi Jane Tao, Jingqiang Zhang. Structure determination of a human virus by the combination of cryo-EM and X-ray crystallography. Biophysics Reports, 2016, 2(2-4): 55-68. doi: 10.1007/s41048-016-0027-2

Citation:

Zheng Liu, Tom S. Y. Guu, Jianhao Cao, Yinyin Li, Lingpeng Cheng, Yizhi Jane Tao, Jingqiang Zhang. Structure determination of a human virus by the combination of cryo-EM and X-ray crystallography. Biophysics Reports, 2016, 2(2-4): 55-68. doi: 10.1007/s41048-016-0027-2

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Structure determination of a human virus by the combination of cryo-EM and X-ray crystallography

doi: 10.1007/s41048-016-0027-2

1 Department of Biophysics, Health Science Centre, Peking University, Beijing 100191, China
2 Department of BioSciences, Rice University, Houston, TX 77005, USA
3 School of Life sciences, Sun Yat-sen University, Guangzhou 510275, China
4 School of Life Science, Tsinghua University, Beijing 100084, China
5 State Key Laboratory of Organ Failure Research, Institute of Antibody Engineering, School of Biotechnology, Southern Medical University, Guangzhou 510515, China
6 Present address:Department of Biochemistry and Molecular Biophysics, Columbia University, New York 10032, USA

Funds: This work was supported by a grant from The National Nature Science Foundation of China (31170691) and the Robert A. Welch Foundation (C-1565 to YJT).

More Information

Corresponding author: Yizhi Jane Tao, Jingqiang Zhang
Received Date: 14 November 2015
Rev Recd Date: 17 February 2016
Publish Date: 28 February 2016

Abstract

Abstract

Virus 3D atomic structures provide insight into our understanding of viral life cycles and the development of antiviral drugs. X-ray crystallography and cryo-EM have been used to determine the atomic structure of viruses. However, limited availability of biological samples, biosafety issues due to virus infection, and sometimes inherent characteristics of viruses, pose difficulties on combining both methods in determining viral structures. These have made solving the high resolution structure of some medically important viruses very challenging. Here, we describe our recently employed protocols for determining the high-resolution structure of the virus-like particle of hepatitis E virus (HEV), a pathogen of viral hepatitis in human. These protocols include utilizing recombinant baculovirus system to generate sufficient amount of virus particles, single-particle cryo-EM to get an intermediate resolution structure as a phasing model, and X-ray crystallography for final atomic structure determination. Our protocols have solved the hepatitis E virus structure to the resolution of 3.5 Å. The combined methodology is generally applicable to other human infectious viruses.
- Structure determination,
- Cryo-EM,
- X-ray crystallography,
- Human virus

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References(26)

References

Balayan MS, Andjaparidze AG, Savinskaya SS, Ketiladze ES, Braginsky DM, Savinov AP, Poleschuk VF (1983) Evidence for a virus in non-A, non-B hepatitis transmitted via the fecaloral route. Intervirology 20:23-31

Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Crystallography & NMR system:a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54:905-921

Collaborative CP (1994) The CCP4 suite:programs for protein crystallography. Acta Crystallogr Sect D, Biol Crystallogr 50:760

Dodson EJ (2001) Using electron-microscopy images as a model for molecular replacement. Acta Crystallogr D 57:1405-1409.doi: 10.1107/S0907444901013415

Guu TS, Liu Z, Ye Q, Mata DA, Li K, Yin C, Zhang J, Tao YJ (2009)Structure of the hepatitis E virus-like particle suggests mechanisms for virus assembly and receptor binding. Proc Natl Acad Sci USA 106:12992-12997. doi:10.1073/pnas. 0904848106

Jiang W, Guo F, Liu Z (2012) A graph theory method for determination of cryo-EM image focuses. J Struct Biol 180:343-351. doi: 10.1016/j.jsb.2012.07.005

Jones T (1992) A set of averaging programs. In:Dodson E, Gover S, Wolf W (eds) Molecular replacement. SERC Daresbury Laboratory, Warrington, pp 91-105

Jones TA, Zou JY, Cowan SWT, Kjeldgaard M (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr Sect A:Found Crystallogr 47:110-119

Kleywegt GJ, Jones TA (1996) xdlMAPMAN and xdlDATAMANprograms for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets. Acta Crystallogr D Biol Crystallogr 52:826-828

Li TC, Yamakawa Y, Suzuki K, Tatsumi M, Razak MA, Uchida T, Takeda N, Miyamura T (1997) Expression and self-assembly of empty virus-like particles of hepatitis E virus. J Virol 71:7207-7213

Li S, Tang X, Seetharaman J, Yang C, Gu Y, Zhang J, Du H, Shih JW, Hew CL, Sivaraman J, Xia N (2009) Dimerization of hepatitis E virus capsid protein E2s domain is essential for virus-host interaction. PLoS Pathog 5:e1000537. doi: 10.1371/journal.ppat.1000537

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

Liu Z, Zhang J-J (2014) Revolutionary breakthrough of structure determination-recent advances of electron direct detection device application in cryo-EM. Acta Biophys Sin 30:1-12

Liu H, Cheng L, Zeng S, Cai C, Zhou ZH, Yang Q (2008) Symmetryadapted spherical harmonics method for high-resolution 3D single-particle reconstructions. J Struct Biol 161:64-73.doi: 10.1016/j.jsb.2007.09.016

Liu Z, Tao YJ, Zhang J (2011) Structure and function of the hepatitis E virus capsid related to hepatitis E pathogenesis.In:Mukomolov DS (ed) Viral hepatitis-selected issues of pathogenesis and diagnostics. InTech, New York, pp 141-152

Liu Z, Guo F, Wang F, Li TC, Jiang W (2016) 2.9 Å resolution cryo-EM 3D reconstruction of close-packed virus particles. Structure 24:319-328. doi: 10.1016/j.str.2015.12.006

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

Navaza J (2008) Combining X-ray and electron-microscopy data to solve crystal structures. Acta Crystallogr Sect D, Biol Crystallogr 64:70-75. doi: 10.1107/S0907444907053334

Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Method Enzymol 276:307-326. doi: 10.1016/S0076-6879(97)76066-X

Read RJ, Kleywegt GJ (2001) Density modification:theory and practice. In:Turk D, Johnson L (eds) Methods in macromolecular crystallography. IOS Press, Amsterdam, pp 123-135

Stein PE, Boodhoo A, Armstrong GD, Cockle SA, Klein MH, Read RJ (1994) The crystal structure of pertussis toxin.Structure 2:45-57

Tang X, Yang C, Gu Y, Song C, Zhang X, Wang Y, Zhang J, Hew CL, Li S, Xia N, Sivaraman J (2011) Structural basis for the neutralization and genotype specificity of hepatitis E virus.Proc Natl Acad Sci USA 108:10266-10271. doi:10.1073/pnas. 1101309108

Ten Eyck LF (1977) Efficient structure-factor calculation for large molecules by the fast Fourier transform. Acta Crystallogr Sect A 33:486-492

Tong L, Rossmann MG (1997) Rotation function calculations with GLRF program. Methods Enzymol 276:594

Xing L, Li TC, Mayazaki N, Simon MN, Wall JS, Moore M, Wang CY, Takeda N, Wakita T, Miyamura T, Cheng RH (2010) Structure of hepatitis E virion-sized particle reveals an RNA-dependent viral assembly pathway. J Biol Chem 285:33175-33183.doi: 10.1074/jbc.M110.106336

Yamashita T, Mori Y, Miyazaki N, Cheng RH, Yoshimura M, Unno H, Shima R, Moriishi K, Tsukihara T, Li TC, Takeda N, Miyamura T, Matsuura Y (2009) Biological and immunological characteristics of hepatitis E virus-like particles based on the crystal structure. Proc Natl Acad Sci USA 106:12986-12991. doi:10. 1073/pnas.0903699106

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