AI Chat Paper
Note: Please note that the following content is generated by AMiner AI. SciOpen does not take any responsibility related to this content.
{{lang === 'zh_CN' ? '文章概述' : 'Summary'}}
{{lang === 'en_US' ? '中' : 'Eng'}}
Chat more with AI
PDF (1.7 MB)
Collect
Submit Manuscript AI Chat Paper
Show Outline
Outline
Show full outline
Hide outline
Outline
Show full outline
Hide outline
Protocol | Open Access

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

Zheng Liu1,6Tom S. Y. Guu2Jianhao Cao3,5Yinyin Li3Lingpeng Cheng4Yizhi Jane Tao2( )Jingqiang Zhang3( )
Department of Biophysics, Health Science Centre, Peking University, Beijing 100191, China
Department of BioSciences, Rice University, Houston, TX 77005, USA
School of Life sciences, Sun Yat-sen University, Guangzhou 510275, China
School of Life Science, Tsinghua University, Beijing 100084, China
State Key Laboratory of Organ Failure Research, Institute of Antibody Engineering, School of Biotechnology,Southern Medical University, Guangzhou 510515, China
Present address: Department of Biochemistry and Molecular Biophysics, Columbia University, New York 10032, USA
Show Author Information

Graphical 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.

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 fecal-oral 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:10.1107/S0907444901013415

 

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 xdlDATAMAN-programs 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 E2 s 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) Symmetry-adapted 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

 
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. doi:10.1016/S0076-6879(97)76066-X
 

Stein PE, Boodhoo A, Armstrong GD, Cockle SA, Klein MH, Read RJ, (1994) The crystal structure of pertussis toxin. Structure 2:45-57. doi:10.1073/pnas.1101309108

 
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
Biophysics Reports
Pages 55-68
Cite this article:
Liu Z, Guu TSY, Cao J, et al. Structure determination of a human virus by the combination of cryo-EM and X-ray crystallography. Biophysics Reports, 2016, 2(2-4): 55-68. https://doi.org/10.1007/s41048-016-0027-2

325

Views

8

Downloads

4

Crossref

0

Scopus

0

CSCD

Altmetrics

Received: 14 November 2015
Accepted: 17 February 2016
Published: 02 September 2016
© The Author(s) 2016

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Return