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Backbone structure of the infectious ε15 virus capsid revealed by electron cryomicroscopy

Abstract

A half-century after the determination of the first three-dimensional crystal structure of a protein1, more than 40,000 structures ranging from single polypeptides to large assemblies have been reported2. The challenge for crystallographers, however, remains the growing of a diffracting crystal. Here we report the 4.5-Å resolution structure of a 22-MDa macromolecular assembly, the capsid of the infectious epsilon15 (ε15) particle, by single-particle electron cryomicroscopy. From this density map we constructed a complete backbone trace of its major capsid protein, gene product 7 (gp7). The structure reveals a similar protein architecture to that of other tailed double-stranded DNA viruses, even in the absence of detectable sequence similarity3,4. However, the connectivity of the secondary structure elements (topology) in gp7 is unique. Protruding densities are observed around the two-fold axes that cannot be accounted for by gp7. A subsequent proteomic analysis of the whole virus identifies these densities as gp10, a 12-kDa protein. Its structure, location and high binding affinity to the capsid indicate that the gp10 dimer functions as a molecular staple between neighbouring capsomeres to ensure the particle’s stability. Beyond ε15, this method potentially offers a new approach for modelling the backbone conformations of the protein subunits in other macromolecular assemblies at near-native solution states.

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Figure 1: Cryo-EM image and three-dimensional map of bacteriophage ε15.
Figure 2: Model of gp7 monomer.
Figure 3: Capsid model and interactions of gp7.
Figure 4: Gp10, a molecular staple.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The three-dimensional density map has been deposited into the EBI–MSD EMD database with accession number EMD-5003. The backbone model has also been deposited in the Protein Data Bank with accession number 3C5B.

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Acknowledgements

We thank D. Braun, P. Smith and B. Loftis; D. Sierkowski, P. Mikeal and S. Wilson for their support with the Condor computing system; and R. H. Goradia and M. Dougherty for digitizing the image data and preparing the Supplementary Movies respectively. This work was supported by grants from the National Institutes of Health and the National Science Foundation.

Author Contributions M.L.B. and W.J. conducted the structural analysis and contributed equally to this work. W.J. performed the image processing and reconstructions. J.J. collected the cryo-EM image data. P.R.W. performed the biochemical purification and characterization of ε15. M.L.B., W.J., P.R.W., J.K. and W.C. interpreted the results and wrote the manuscript.

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Correspondence to Wen Jiang or Wah Chiu.

Supplementary information

Supplementary Information

The file contains Supplementary Notes divided into two parts: Supplement 1 which discusses constructing C backbone models for gp7 and Supplement 2 discussing structural comparison between ε15 and HK97 capsid proteins, followed by additional references. The file also contains Supplementary Figures 1-8 with Legends. (PDF 28763 kb)

Supplementary Movie 1

The file contains Supplementary Movie 1 showing 4.5 Å cryo-EM map of ε15 is dissected to show the whole capsid, an asymmetric unit, and a single gp7 monomer (MOV 1887 kb)

Supplementary Movie 2

The file contains Supplementary Movie 2 showing C backbone trace of ε15 gp7 monomer. (MOV 1895 kb)

Supplementary Movie 3

The file contains Supplementary Movie 3 showing ε15 gp7 capsid model. (MOV 1845 kb)

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Jiang, W., Baker, M., Jakana, J. et al. Backbone structure of the infectious ε15 virus capsid revealed by electron cryomicroscopy. Nature 451, 1130–1134 (2008). https://doi.org/10.1038/nature06665

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