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. 2007 Feb;157(2):356-64.
doi: 10.1016/j.jsb.2006.09.002. Epub 2006 Sep 16.

Structural analysis of viral nucleocapsids by subtraction of partial projections

Ying Zhang  1 , Victor A Kostyuchenko, Michael G Rossmann
Affiliations

Structural analysis of viral nucleocapsids by subtraction of partial projections

Ying Zhang et al. J Struct Biol. 2007 Feb.

Abstract

The nucleocapsid of flavivirus particles does not have a recognizable capsid structure when using icosahedral averaging for cryo-electron microscopy structure determinations. The apparent absence of a definitive capsid structure could be due to a lack of synchronization of the symmetry elements of the external glycoprotein layer with those of the core or because the nucleocapsid does not have the same structure within each particle. A technique has been developed to determine the structure of the capsid, and possibly also of the genome, for icosahedral viruses, such as flaviviruses, using cryo-electron microscopy. The method is applicable not only to the analyses of viral cores, but also to the missing structure of multi-component complexes due to symmetry mismatches. The density contributed by external glycoprotein and membrane layers, derived from previously determined three-dimensional icosahedrally averaged reconstructions, was subtracted from the raw images of the virus particles. The resultant difference images were then used for a three-dimensional reconstruction. After appropriate test data sets were constructed and tested, the procedure was applied to examine the nucleocapsids of flaviviruses, which showed that there is no distinct protein density surrounding the genome. Furthermore, there was no evidence of any icosahedral symmetry within the nucleocapsid core.

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Figures

Fig. 1
Fig. 1
Simulated images of the test data sets. (A) A representative theoretical projection of the CpMV test data set. (B) The same as (A) but with added noise to obtain the signal-to-noise ratio of 1:1. (C) The same as (B) after applying the CTF. (D) The same as (C) except more noise was added to the image to make the signal-to-noise ratio of 1:20. (E), (F), (G), and (H) correspond to (A), (B), (C), and (D), but use the ribosome test data set. The scale bar represents 100 Å.
Fig. 2
Fig. 2
Test using the CpMV data set. (A) Four class averages of difference images that have the highest FSCs. (B) Projections of the atomic structure calculated to 20 Å resolution with orientations corresponding to (A). (C) 3D reconstruction of the CpMV core using the difference images. (D) The structure of CpMV calculated to 25 Å resolution in the same orientation as (C). The scale bar represents 100 Å.
Fig. 3
Fig. 3
Test using the ribosome data set. (A) Four class averages of difference images that have the highest FSCs. (B) Projections of the atomic structure calculated to 20 Å resolution with orientations corresponding to (A). (C) 3D reconstruction of the ribosome core using the difference images. (D) The structure of ribosome calculated to 25 Å resolution in the same orientation as (C). The scale bar represents 100 Å.
Fig. 4
Fig. 4
Five selected class averages that have the highest FSCs: (A) nucleocapsid cores of immature DENV, (B) nucleocapsid cores of mature DENV, and (C) immature DENV. The scale bar represents 100 Å.
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References

    1. Allison SL, Stadler K, Mandl CW, Kunz C, Heinz FX. Synthesis and secretion of recombinant tick-borne encephalitis virus protein E in soluble and particulate form. J Virol. 1995;69:5816–5820. - PMC - PubMed
    1. Baker TS, Cheng RH. A model-based approach for determining orientations of biological macromolecules imaged by cryoelectron microscopy. J Struct Biol. 1996;116:120–130. - PubMed
    1. Baker TS, Newcomb WW, Booy FP, Brown JC, Steven AC. Three-dimensional structures of maturable and abortive capsids of equine herpesvirus 1 from cryoelectron microscopy. J Virol. 1990;64:563–573. - PMC - PubMed
    1. Baker TS, Olson NH, Fuller SD. Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs. Microbiol Mol Biol Rev. 1999;63:862–922. - PMC - PubMed
    1. Booy FP, Newcomb WW, Trus BL, Brown JC, Baker TS, Steven AC. Liquid-crystalline, phage-like packing of encapsidated DNA in herpes simplex virus. Cell. 1991;64:1007–1015. - PMC - PubMed

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