Cryo-EM structure of the mature dengue virus at 3.5-Å resolution

Nature Structural and Molecular Biology

Volumn 20, Issue 1, 2013, Pages 105-110

  Zhang, Xiaokang ^a,b,c,d   Ge, Peng ^a,b   Yu, Xuekui ^a,b   Brannan, Jennifer M ^b,f   Bi, Guoqiang ^c,d   Zhang, Qinfen ^e   Schein, Stan ^a   Hong Zhou, Z ^a,b,c,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

^c UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^d UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^e SUN YAT SEN UNIVERSITY   (China)

^f US Army Medical Research Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTIDINE; PROTEIN E; PROTEIN M; UNCLASSIFIED DRUG; VIRUS PROTEIN;

ACIDITY; AMINO TERMINAL SEQUENCE; ARTICLE; CELL MATURATION; CONFORMATIONAL TRANSITION; CRYOELECTRON MICROSCOPY; DENGUE VIRUS; ENDOSOME; NONHUMAN; PH; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN STRUCTURE; TRANS GOLGI NETWORK; VIRION; VIROGENESIS; VIRUS MORPHOLOGY;

AEDES; ANIMALS; CELL LINE; CRYOELECTRON MICROSCOPY; CRYSTALLOGRAPHY, X-RAY; DENGUE VIRUS; HYDROGEN-ION CONCENTRATION; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MEMBRANE PROTEINS; PROTEIN CONFORMATION; TRANS-GOLGI NETWORK; VIRAL ENVELOPE PROTEINS; VIRAL MATRIX PROTEINS; VIRUS ATTACHMENT;

DENGUE VIRUS;

EID: 84872048730     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.2463     Document Type: Article

References (36)

1. WHO. Dengue: Guidelines for Diagnosis, Treatment, Prevention and Control (WHO, Geneva, Switzerland 2009)
2. Borio, L. et al. Hemorrhagic fever viruses as biological weapons: medical and public health management. J. Am. Med. Assoc. 287, 2391-2405 (2002).
3. Yu, I. M. et al. Structure of the immature dengue virus at low pH primes proteolytic maturation. Science 319, 1834-1837 (2008).
4. Li, L. et al. The flavivirus precursor membrane-envelope protein complex: structure and maturation. Science 319, 1830-1834 (2008).
5. Kielian, M. & Rey, F. A. Virus membrane-fusion proteins: more than one way to make a hairpin. Nat. Rev. Microbiol. 4, 67-76 (2006).
6. Harrison, S. C. Viral membrane fusion. Nat. Struct. Mol. Biol. 15, 690-698 (2008).
7. Kuhn, R. J. et al. Structure of dengue virus: implications for flavivirus organization, maturation, and fusion. Cell 108, 717-725 (2002).
8. Zhang, W. et al. Visualization of membrane protein domains by cryo-electron microscopy of dengue virus. Nat. Struct. Biol. 10, 907-912 (2003).
9. Modis, Y., Ogata, S., Clements, D. & Harrison, S. C. A ligand-binding pocket in the dengue virus envelope glycoprotein. Proc. Natl. Acad. Sci. USA 100, 6986-6991 (2003).
10. Modis, Y., Ogata, S., Clements, D. & Harrison, S. C. Structure of the dengue virus envelope protein after membrane fusion. Nature 427, 313-319 (2004).
11. Zhang, Y. et al. Conformational changes of the flavivirus E glycoprotein. Structure 12, 1607-1618 (2004).
12. Plevka, P. et al. Maturation of flaviviruses starts from one or more icosahedrally independent nucleation centres. EMBO Rep. 12, 602-606 (2011).
13. Liu, X., Jiang, W., Jakana, J. & Chiu, W. 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 (2007).
14. Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721-745 (2003).
15. Kaptein, S. J. et al. A derivate of the antibiotic doxorubicin is a selective inhibitor of dengue and yellow fever virus replication in vitro. Antimicrob. Agents Chemother. 54, 5269-5280 (2010).
16. Wang, Q. Y. et al. A small-molecule dengue virus entry inhibitor. Antimicrob. Agents Chemother. 53, 1823-1831 (2009).
17. Cockburn, J. J. et al. Membrane structure and interactions with protein and DNA in bacteriophage PRD1. Nature 432, 122-125 (2004).
18. Zhang, R. et al. 4. 4 A cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus. EMBO J. 30, 3854-3863 (2011).
19. Fritz, R. et al. The unique transmembrane hairpin of flavivirus fusion protein E is essential for membrane fusion. J. Virol. 85, 4377-4385 (2011).
20. Fritz, R., Stiasny, K. & Heinz, F. X. Identification of specific histidines as pH sensors in flavivirus membrane fusion. J. Cell Biol. 183, 353-361 (2008).
21. Kroschewski, H., Sagripanti, J. L. & Davidson, A. D. Identification of amino acids in the dengue virus type 2 envelope glycoprotein critical to virus infectivity. J. Gen. Virol. 90, 2457-2461 (2009).
22. Nelson, S., Poddar, S., Lin, T.-Y. & Pierson, T. C. Protonation of individual histidine residues is not required for the pH-dependent entry of West Nile Virus: evaluation of the "histidine switch" hypothesis. J. Virol. 83, 12631-12635 (2009).
23. Yu, I. M. et al. Association of the pr peptides with dengue virus at acidic pH blocks membrane fusion. J. Virol. 83, 12101-12107 (2009).
24. Zhang, Y. et al. Structures of immature flavivirus particles. EMBO J. 22, 2604-2613 (2003).
25. Gaudin, Y. Reversibility in fusion protein conformational changes. The intriguing case of rhabdovirus-induced membrane fusion. Subcell. Biochem. 34, 379-408 (2000).
26. Lalezari, J. P. et al. A phase II clinical study of the long-term safety and antiviral activity of enfuvirtide-based antiretroviral therapy. AIDS 17, 691-698 (2003).
27. Ludtke, S. J., Baldwin, P. R. & Chiu, W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128, 82-97 (1999).
28. Liang, Y., Ke, E. Y. & Zhou, Z. H. IMIRS: a high-resolution 3D reconstruction package integrated with a relational image database. J. Struct. Biol. 137, 292-304 (2002).
29. Liu, H. et al. Atomic structure of human adenovirus by cryo-EM reveals interactions among protein networks. Science 329, 1038-1043 (2010).
30. Mindell, J. A. & Grigorieff, N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142, 334-347 (2003).
31. Kivioja, T., Ravantti, J., Verkhovsky, A., Ukkonen, E. & Bamford, D. Local average intensity-based method for identifying spherical particles in electron micrographs. J. Struct. Biol. 131, 126-134 (2000).
32. Zhang, J. et al. Mechanism of folding chamber closure in a group II chaperonin. Nature 463, 379-383 (2010).
33. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486-501 (2010).
34. Li, Y. & Zhang, Y. REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins 76, 665-676 (2009).
35. Brunger, A. T. Version 1. 2 of the crystallography and NMR system. Nat. Protoc. 2, 2728-2733 (2007).
36. Ge, P. & Zhou, Z. H. Hydrogen-bonding networks and RNA bases revealed by cryo electron microscopy suggest a triggering mechanism for calcium switches. Proc. Natl. Acad. Sci. USA 108, 9637-9642 (2011).