Volume 25, Issue 10, Pages 1562-1573.e5 (October 2017) Structure of a Reptilian Adenovirus Reveals a Phage Tailspike Fold Stabilizing a Vertebrate Virus Capsid  Rosa Menéndez-Conejero, Thanh H. Nguyen, Abhimanyu K. Singh, Gabriela N. Condezo, Rachel E. Marschang, Mark J. van Raaij, Carmen San Martín  Structure  Volume 25, Issue 10, Pages 1562-1573.e5 (October 2017) DOI: 10.1016/j.str.2017.08.007 Copyright © 2017 Elsevier Ltd Terms and Conditions

Structure 2017 25, 1562-1573.e5DOI: (10.1016/j.str.2017.08.007) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 1 Thermostability of SnAdV-1 (A) Infectivity changes in HAdV-C5 and SnAdV-1 after heating. Data were normalized by dividing the infectious units after heat treatment by the infectious units of the control (unheated) sample. Data from nine experiments represented as mean ± SD. (B) Negative staining EM images showing HAdV-C5 and SnAdV-1 capsids after heating at the indicated temperatures. Scale bar, 100 nm. Structure 2017 25, 1562-1573.e5DOI: (10.1016/j.str.2017.08.007) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 2 Cryo-EM Analysis of SnAdV-1 (A) Representative cryo-EM field. (B) Surface rendering of the SnAdV-1 3D map colored by radius, as indicated by the color scale. The four hexon trimers in an AU are numbered 1–4. (C) Side by side comparison of SnAdV-1 and HAdV-C5 map central sections. Highest protein density is white. Directly observable differences are indicated by letters a to d. White symbols indicate the icosahedral 5-fold (pentagon), 3-fold (triangle), and 2-fold (oval) symmetry axes. See also Figure S1. Structure 2017 25, 1562-1573.e5DOI: (10.1016/j.str.2017.08.007) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 3 SnAdV-1 Internal Minor Coat Proteins (A) A view from inside the capsid showing one AU and its immediate neighborhood. The density map calculated from the hexon and penton pseudo-atomic model is shown in gray and contoured at 0.75σ level. The difference map is radially colored according to the scale shown at the right and rendered at 2.5σ. The icosahedral symmetry axes are indicated by red symbols, and the four hexon trimers are labeled 1–4. Positions where difference densities are described in the text are labeled p1 to p5. A schematic of the AU labeled in the same way is shown in the top left corner for guidance. (B) Difference densities and protein models beneath the vertex region, as seen from inside the viral particle. The structures of HAdV-C5 protein VIII (brown) and IIIa (yellow) are fitted into the EM difference map, shown at a 2.9σ threshold as a blue mesh. The penton base is colored in purple and peripentonal hexons in light pink. The dashed rectangle at the right shows a zoom into a single copy of IIIa. The location of different domains in IIIa and VIII, designated as in Liu et al. (2010), is indicated. (C) The vertex region shown in a transversal cut across the penton. f, fiber. (D) The same region shown in (B) as a zoom in, with the difference map rendered at a lower threshold (2.5σ) and from a point of view deeper inside the virus particle. Unassigned density near IIIa is indicated with black stars. Structure 2017 25, 1562-1573.e5DOI: (10.1016/j.str.2017.08.007) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 4 SnAdV-1 Internal Minor Coat Proteins at the Facet Center (A) Difference densities (2.8σ) and protein models beneath the facet center. Hexons 2 (light cyan), 3 (light green), and 4 (beige) in one AU are labeled. A red star indicates unassigned density between hexons 2 and 4. Two α helices (green) have been modeled in one leaf of the trefoil-like difference density at the facet center. (B and C) Secondary structure prediction for (B) SnAdV-1 LH2, and (C) p32k proteins. α Helices are in red and β strands in green. The p32k protease cleavage site is indicated with a black box. Structure 2017 25, 1562-1573.e5DOI: (10.1016/j.str.2017.08.007) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 5 SnAdV-1 External Minor Coat Proteins and the LH3 Crystal Structure (A) A view from outside the capsid showing one AU and its immediate neighborhood. The density map calculated from the hexon and penton pseudo-atomic model is shown in gray and contoured at 0.75σ level. The difference map is radially colored according to the scale shown at the right and rendered at 2.5σ. The icosahedral symmetry axes are indicated by red symbols, and the four hexon trimers are labeled 1–4. A schematic of the AU labeled in the same way is shown in the top left corner for guidance. f, fiber. (B) Overall view of the LH3 crystal structure seen from the side (left) and top (right). Monomers are colored green, cyan, and magenta. The N and C termini of the cyan subunit are labeled. β Sheets and turns are labeled in the cyan-colored subunit in the top view. PB1 is the β sheet that contains the first β strand of all the β-helical turns, counting from the N terminus. Sheets PB2 and PB3 contain the second and third β strand of the same β-helical turn, respectively. Turns between β strands are named T1 (between PB1 and PB2), T2 (between PB2 and PB3), and T3 (between PB3 and PB1). (C) Illustration of isoleucine, phenylalanine, and asparagine ladders in the LH3 structure. (D) Structure of the bacteriophage P22 tailspike seen from the side; N and C termini are indicated. (E) Bacteriophage P22 and Sf6 tailspikes bound, respectively, to a tetra-saccharide (PDB: 1TYU) and an octa-saccharide (PDB: 4URR) ligand (yellow). For comparison, a surface representation of the LH3 protein is shown in the same color scheme. (F) LH3 surface colored by electrostatic potential as seen from the side (top) and from the capsid surface (bottom). (G) Fitting of the LH3 crystal structure (gold) into the cryo-EM difference map (blue mesh), rendered at 2.5σ in a transversal view at the 3-fold icosahedral axis. Two 3-fold-related hexon trimers are shown in light green. The black star indicates the position of the first residue in the crystal structure (Ser26). Residues involved in interactions with the hexon towers are depicted in red in one of the LH3 monomers. (H) The LH3 trimer at the icosahedral 3-fold axis (black triangle) and the three symmetry-related hexon trimers as seen from outside the capsid. Each LH3 monomer contacts two different hexon trimers, one via the T2 and another via the T3 turns. Structure 2017 25, 1562-1573.e5DOI: (10.1016/j.str.2017.08.007) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 6 Schematics Illustrating the Different Protein Networks in Mast- and Atadenoviruses One facet in the icosahedral particle is depicted. HAdV-C5 minor coat protein positions are according to Liu et al. (2010). Structure 2017 25, 1562-1573.e5DOI: (10.1016/j.str.2017.08.007) Copyright © 2017 Elsevier Ltd Terms and Conditions