Volume 18, Issue 2, Pages 161-170 (April 2005) The Structure of the Bacteriophage PRD1 Spike Sheds Light on the Evolution of Viral Capsid Architecture  Michael C. Merckel, Juha T. Huiskonen, Dennis H. Bamford, Adrian Goldman, Roman Tuma  Molecular Cell  Volume 18, Issue 2, Pages 161-170 (April 2005) DOI: 10.1016/j.molcel.2005.03.019 Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 1 Structure of the P5 Knob Domain (A) Section through the P5T map (MAD-phased map in red, refined 2FoFc map in blue) together with stick model of the polypeptide (yellow). (B) Secondary structure assignment for P5T in the full-length sequence using amino acid numbering according to the gene (shown below the sequence) (Bamford and Bamford, 1990). The crystallized C-terminal fragment P5C begins after the collagenase cleavage site (red arrow, first residue Gly136) The position of a flexible glycine hinge is also indicated. The portion of the shaft, which was resolved in the rhombohedral crystal, is marked with a black arrow above the sequence. The alignment figure was produced by using the program SecSeq (D.E. Brodersen, unpublished software, http://xray.imsb.au.dk/∼deb/secseq). (C) Stereo ribbon diagram of the P5T trimer viewed down the 3-fold axis. Each subunit is shown in a different color. The N terminus is labeled. (D) Fitting of the P5T high-resolution structure into the low-resolution envelope of the P5C. The dummy atom SAXS model (Sokolova et al., 2001) is represented by red spheres. The left panel shows the end-on view, and the right panel corresponds to a side view. Fitting was done with the program SUPCOMB (Kozin and Svergun, 2001). Molecular Cell 2005 18, 161-170DOI: (10.1016/j.molcel.2005.03.019) Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 2 Structure of the P5CΔG8 Trimer (A) Stereo ribbon diagram of P5CΔG8 structure with the shaft domain delineated by a double-headed arrow. (B) Shaft repeats of adenovirus (van Raaij et al., 1999b) (left) and reovirus (Chappell et al., 2002) (right) compared with PRD1. (C) Comparison of the β spiral repeats. Cα trace of the P5CΔG8 repeat is in red, the five adenovirus Ad2 fiber shaft repeats are in green (PDB access code 1QUI [van Raaij et al., 1999b], repeat 22 is only partial) and the three repeats of the reovirus σ1 tail are in blue (PDB access code 1KKE, [Chappell et al., 2002]). Overlay was performed manually with LSQMAN (Kleywegt and Jones, 1997). (D) Side view of the shaft domain with salt bridges highlighted by dotted lines. Only two chains (A in green and B in red) are shown for clarity. Molecular Cell 2005 18, 161-170DOI: (10.1016/j.molcel.2005.03.019) Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 3 Comparison of the P5T Fold with TNF-α (A) Ribbon diagram of the P5T monomer (blue) backbone superposed onto the TNF structure (PDB accession code 2TNF, [Bodmer et al., 2002], red) by using DALI. (B) Interaction between subunits mapped onto the subunit interface. (Top) Percentage of buried surface (0% = red, 100% = blue). (Bottom) Interacting residues highlighted by type: polar, blue; hydrophobic, yellow; main chain, white; and charged, red. Figure was made with GRASP (Nicholls et al., 1991). Molecular Cell 2005 18, 161-170DOI: (10.1016/j.molcel.2005.03.019) Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 4 Relationship of the P5T Structure to the PRD1 Coat Protein Domains (A) The eight-stranded topology of the PRD1 coat protein (P3) domains is interchangeable with the ten-stranded topology of P5T via insertion/deletion of the A′-B′ strands (green). The connection between A-B strands in P3 is shown as a yellow dashed line. (B) Structural alignment of the P5T subunit (blue with A′-B′ strands in green) and P3 domain V1 (red) and V2 (teal), (PDB accession code 1HX6, [Benson et al., 2002]). The β sheet angles are indicated. Molecular Cell 2005 18, 161-170DOI: (10.1016/j.molcel.2005.03.019) Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 5 Comparison between the Adenovirus and PRD1 Knobs (A) Structural alignment of the P5T3 (red) and adenovirus knob (blue, 1KNB, [Xia et al., 1994]). Left panel shows side view of the monomer, right panel shows the trimer viewed down the 3-fold axis. (B) Comparison of hydrophobic core packing for the adenovirus knob and hexon domains. The angle of the of the β sheets are indicated. (C) Relationship between the P5T topology (left) and adenovirus knob fold (right). The deletions in P5T needed to obtain the adenovirus knob topology are dashed. Molecular Cell 2005 18, 161-170DOI: (10.1016/j.molcel.2005.03.019) Copyright © 2005 Elsevier Inc. Terms and Conditions