Volume 26, Issue 2, Pages 238-248.e3 (February 2018) Structure of the Marine Siphovirus TW1: Evolution of Capsid-Stabilizing Proteins and Tail Spikes  Zhiqing Wang, Stephen C. Hardies, Andrei Fokine, Thomas Klose, Wen Jiang, Byung Cheol Cho, Michael G. Rossmann  Structure  Volume 26, Issue 2, Pages 238-248.e3 (February 2018) DOI: 10.1016/j.str.2017.12.001 Copyright © 2017 Elsevier Ltd Terms and Conditions

Structure 2018 26, 238-248.e3DOI: (10.1016/j.str.2017.12.001) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 1 Sequence of the Tail Protein Genes in the Genomes of Siphophages TW1, λ, and SPP1 The sequences are color coded according to gene function. The length of each gene is proportional to the number of nucleotides in the gene. Numbers and letters refer to the name of the gene product. Structure 2018 26, 238-248.e3DOI: (10.1016/j.str.2017.12.001) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 2 Structure of the TW1 Capsid (A) A cryo-EM image of TW1 phages. (B) Diagram showing one pentamer and two hexamers of the major capsid protein. The decoration protein trimers are shown as circles. The icosahedral asymmetric unit is colored gray and is limited by the green 2-, 3-, and 5-fold symmetry axes. (C) Icosahedrally averaged cryo-EM map of the TW1 capsid at 3.6 Å resolution. Coloring is radial based as indicated by the color bar. The numbers in the color bar represent the distance from the center of the virus to the surface. One asymmetric unit is outlined by the black triangle. (D) Atomic structure of the TW1 asymmetric unit containing seven molecules of the major capsid protein, gp57∗, and seven molecules of the decoration protein, gp56, shown as ribbon diagrams. The gp57∗ molecules are colored yellow and the gp56 molecules are red. (E and F) Ribbon diagrams of the bacteriophage HK97 major capsid protein (E) and the TW1 major capsid protein, gp57∗ (F). The A domain of gp57∗ has an additional helix shown in red. The G loop of HK97 and of TW1 are also shown in red, indicating that TW1 has a longer G loop than that in HK97 and that they have different conformations. See also Figures S1 and S2; Table S1. Structure 2018 26, 238-248.e3DOI: (10.1016/j.str.2017.12.001) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 3 The TW1 Decoration Protein, gp56 (A) Top views of the gp56 trimer. The N-terminal domains of the gp56 molecules (residues 1–86) are colored blue. The C-terminal domains of gp56 (residues 87–148) are colored red. (B) Side view of the gp56 monomer. (C) Superposition of the N-terminal and C-terminal domains of gp56 shown as a stereo diagram. (D) Superposition of the N-terminal domain of gp56 onto the N-terminal region of phage λ gpD (residues 23–78, yellow, PDB: 1TD4). (E) Superposition of the C-terminal domain of gp56 onto the N-terminal region of phage λ gpD (yellow). See also Figure S2 and Table S2. Structure 2018 26, 238-248.e3DOI: (10.1016/j.str.2017.12.001) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 4 Structure of the TW1 Portal and Neck (A) Cryo-EM map showing the TW1 head and neck. Coloring is radial based, as indicated by the color bar. The numbers in the color bar represent the distance from the center of the capsid to the surface. (B) Central section of the cryo-EM map using a grayscale representation in which the lowest density is black and the highest density is white. (C) Structures of the SPP1 portal protein (magenta, PDB: 2JES) and the HK97 neck protein, gp6 (light blue, PDB: 3JVO), fitted into the cryo-EM map. Structure 2018 26, 238-248.e3DOI: (10.1016/j.str.2017.12.001) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 5 Structure of the TW1 Tail-Spike Complex (A) Side view of the tail-spike complex cryo-EM map. (B) Top view of the tail-spike complex cryo-EM map. (C) Bottom view of the tail-spike complex cryo-EM map. The six tail spikes, gp19, are shown in light blue, and the central tail tube is shown in dark blue. (D) Structure of the phage P22 tail-portal complex (reproduced from Lander et al., 2009a). (E) Structure of the phage Sf6 tail complex. (F) Structure of the phage HK620 tail-spike protein (PDB: 4YEJ) fitted into the TW1 density. (G) Structure of the phage λ tail-tube protein, gpV (PDB: 2K4Q), fitted into the TW1 density. Structure 2018 26, 238-248.e3DOI: (10.1016/j.str.2017.12.001) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 6 Structure of the TW1 Virion (A) Model of the entire virion based on the cryo-EM reconstructions of the head and tail. (B) Schematic representation of the virion showing the positions of the structural proteins. Structure 2018 26, 238-248.e3DOI: (10.1016/j.str.2017.12.001) Copyright © 2017 Elsevier Ltd Terms and Conditions