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3.88 Å structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy

Abstract

Cytoplasmic polyhedrosis virus (CPV) is unique within the Reoviridae family in having a turreted single-layer capsid contained within polyhedrin inclusion bodies, yet being fully capable of cell entry and endogenous RNA transcription1,2,3,4. Biochemical data have shown that the amino-terminal 79 residues of the CPV turret protein (TP) is sufficient to bring CPV or engineered proteins into the polyhedrin matrix for micro-encapsulation5,6. Here we report the three-dimensional structure of CPV at 3.88 Å resolution using single-particle cryo-electron microscopy. Our map clearly shows the turns and deep grooves of α-helices, the strand separation in β-sheets, and densities for loops and many bulky side chains; thus permitting atomic model-building effort from cryo-electron microscopy maps. We observed a helix-to-β-hairpin conformational change between the two conformational states of the capsid shell protein in the region directly interacting with genomic RNA. We have also discovered a messenger RNA release hole coupled with the mRNA capping machinery unique to CPV. Furthermore, we have identified the polyhedrin-binding domain, a structure that has potential in nanobiotechnology applications.

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Figure 1: Overall structure of the CPV capsid.
Figure 2: A conformational change between CSP-A and CSP-B: implication for packing and sliding of the dsRNA genome.
Figure 3: Nascent mRNA release hole coupled with the GTase active site of TP in a way unique to CPV.
Figure 4: Location and structure of the unique polyhedrin-binding domain (PBD) of TP.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The cryo-electron microscopy density map has been deposited to the EM Data Bank with accession codes EMD-1508. Coordinates for CSP-A, CSP-B and the N-terminal two domains of TP have been deposited in the Protein Data Bank with accession code 3CNF.

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Acknowledgements

This research is supported in part by grants from NIH and the Welch Foundation. We are grateful to W. Chiu for his advice and support of this project. We thank Y. Liang, J. Jakana, M. Baker and W. Chiu for their participation at the preliminary stage of this project; J.-Q. Zhang for providing the CPV-containing polyhedra sample; I. Atanasov for assistance during cryo-electron microscopy imaging; X. Zhang for graphics illustration; and P. Lo for reading our manuscript.

Author Contributions X.Y. and Z.H.Z. collected the cryo-electron microscopy data; X.Y. processed the data; L.J. built the models; all authors participated in the structure interpretation and manuscript preparation.

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Correspondence to Z. Hong Zhou.

Supplementary information

Supplementary information

The file contains Supplementary Notes, Supplementary Table 1, Legends to Supplementary Movies 1-9 and Supplementary Figures 1-10 with Legends. (PDF 6504 kb)

Supplementary information

The file contains Supplementary Movie 1 showing overall structure of the CPV capsid at 3.88?Å resolution. (AVI 17509 kb)

Supplementary information

The file contains Supplementary Movie 2 showing an extracted helical density from CSP?B superimposed with the C? trace of a standard ??helix, showing the clear turns, the deep grooves and the densities for side?chains revealed by the cryoEM map (AVI 296723 kb)

Supplementary information

The file contains Supplementary Movie 3 showing an extracted density superimposed with the C? traces of CSP?A, showing the separation of the two ? strands. (MPG 36310 kb)

Supplementary information

The file contains Supplementary Movie 4 showing an extracted asymmetric unit from the 3.88?Å resolution density map. (AVI 43247 kb)

Supplementary information

The file contains Supplementary Movie 5 showing density map of CSP?A (blue) and CSP?B (purple) with dsRNA models (red), showing three shallow grooves in the inner sides of both CSP?A and CSP?B. All three grooves are well aligned between CSP?A and CSP?B, forming sliding tracks for RNA. (AVI 15459 kb)

TSupplementary information

The file contains Supplementary Movie 6 showing one TP pentamer (gray), showing that the central chamber of the turret is plugged in by the hemagglutinin?like "A spike" (yellow density). (AVI 41392 kb)

Supplementary information

The file contains Supplementary Movie 7 showing C? models of one CSP?B (cyan), two CSP?As (red and orange), and two GTase domains (blue and light blue), showing the mRNA releasing and capping pathway. (AVI 27212 kb)

Supplementary information

The file contains Supplementary Movie 8 showing Shaded surface representation of TP, showing the two methylase domains (purple), GTase domain (blue), and CPV's unique polyhedrin?binding domain (orange). (AVI 37200 kb)

Supplementary information

The file contains Supplementary Movie 9 showing view of one entire turret, showing the orientation and position of one TP in the turret. (AVI 7379 kb)

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Yu, X., Jin, L. & Zhou, Z. 3.88 Å structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy. Nature 453, 415–419 (2008). https://doi.org/10.1038/nature06893

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