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A virus that infects a hyperthermophile encapsidates A-form DNA

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Science  22 May 2015:
Vol. 348, Issue 6237, pp. 914-917
DOI: 10.1126/science.aaa4181
  • Fig. 1 Cryo-EM and 3D reconstruction of SIRV2.

    (A) Micrograph showing SIRV2 virions in vitreous ice. Scale bar, 1000 Å. (B) Side view of the reconstructed virion with a ribbon model for the protein (magenta). The asymmetric unit in the virion contains a protein dimer, and one is shown with one chain in yellow and the other in green. (C) Cutaway view showing the hollow lumen with the all α-helical protein segments that line the lumen. These α helices wrap around the dsDNA (blue) and encapsidate it. (D) Close-up view of the region shown within the rectangle in (C).

  • Fig. 2 The refined atomic model in the 3D reconstruction.

    (A) The density allows accurate tracing of the nucleotide chain. (B) The interface between helices within the asymmetric unit features large numbers of aromatic residues, which aid in correct registration of the sequence. (C) Side chains at the protein-DNA interface are well defined in density.

  • Fig. 3 The SIRV2 protein dimer helices fully encapsulate the DNA.

    (A) Three asymmetric units of the virion are shown, illustrating how the N-terminal helices wrap around the DNA, forming antiparallel helix-helix packing. (B) Side view. (C) Surface view of the protein (using a 1.4 Å probe radius). (D) The right-handed solenoidal supercoiling of the DNA, with three turns shown.

  • Fig. 4 Overview of protein-DNA contacts in the virion.

    (A) The protein-DNA interface is mainly polar, with largely Arg and Lys side chains contacting phosphate groups in the DNA. (B) Side view. (C) Schematic indicating all of the polar protein-DNA contacts. The coloring of each subunit is the same as in (A) and (B). (D) A multiple sequence alignment with related archaeal rod-shaped viruses indicates that all of these contacts are well conserved (29). SIRV2, Sulfolobus islandicus rod-shaped virus 2; ARV1, Acidianus rod-shaped virus 1; SRV, Stygiolobus rod-shaped virus; SMRV1, Sulfolobales Mexican rudivirus 1. The yellow boxes indicate the residues that are interacting with the DNA backbones.

Supplementary Materials

  • A virus that infects a hyperthermophile encapsidates A-form DNA

    Frank DiMaio, Xiong Yu, Elena Rensen, Mart Krupovic, David Prangishvili, Edward H. Egelman

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    • Materials and Methods
    • Figs. S1 to S5
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