Volume 16, Issue 5, Pages 673-685 (December 2004) Does Common Architecture Reveal a Viral Lineage Spanning All Three Domains of Life?  Stacy D. Benson, Jaana K.H. Bamford, Dennis H. Bamford, Roger M. Burnett  Molecular Cell  Volume 16, Issue 5, Pages 673-685 (December 2004) DOI: 10.1016/j.molcel.2004.11.016

Figure 1 X-Ray Crystal Structures of Viral Double-Barrel Trimeric Major Coat Proteins (A) P3 of bacteriophage PRD1 (394 residues; PDB code 1hx6; Benson et al., 2002), (B) Hexon of adenovirus type 5 (Ad5; 951 residues; PDB code 1p30; Rux et al., 2003), and (C) Vp54 of Paramecium bursaria chlorella virus 1 (PBCV-1; 436 residues; PDB code 1m3y; Nandhagopal et al., 2002). The eight β strands and a flanking α-helix are displayed for the first (green) and second (blue) jelly rolls, and the individual strands are labeled (B1-I1 and B2-I2, respectively). The N- and C-terminal positions are marked, along with the first and last residues modeled in the structures. The four major loops (DE1, FG1, DE2, and FG2), the jelly roll separation domain (VC) and the residue numbers for the unobserved parts of the molecule (<…>) are labeled in Ad5 hexon. In Ad5 hexon, the VC domain and the DE2 loop separate the jelly rolls to produce a molecule with a broader base compared to PRD1 P3 and PBCV-1 Vp54. PBCV-1 Vp54 contains N linked sugars (magenta). Molecular Cell 2004 16, 673-685DOI: (10.1016/j.molcel.2004.11.016)

Figure 2 Comparison of the Major Coat Proteins for Bacteriophages Bam35 and PRD1 (A) A CLUSTAL X (Thompson et al., 1997) sequence alignment of the corresponding major coat proteins (PRD1, GenBank accession number AAA32466 and Bam35, AAP83487) with identical residues boxed in black and similar residues in gray. The secondary structure determined from the X-ray structure of PRD1 P3 is shown above the alignment with α helices represented by cylinders and β strands by arrows. The secondary elements involved in the jelly rolls are colored as in Figure 1A. (B) The Bam35 P3 model based on a Swiss-PdbViewer (Guex and Peitsch, 1997) threading of its sequence onto the structure of PRD1 P3 (Benson et al., 2002). In the Bam35 model, areas of the sequence that do not correspond to sections in PRD1 P3 were connected with the loop database in Swiss-PdbViewer. A molecular dynamics energy minimization in water was performed for the Bam35 P3 model with GROMACS (Berendsen et al., 1995; Lindahl et al., 2001). Conserved (black) and similar (gray) residues are shown. (C) The PRD1 P3 X-ray model showing that insertions with respect to the Bam35 P3 sequence (red) occur in the loops and the C2 strand. Figure (A) produced with ALLSCRIPT (Barton, 1993) and (B) and (C) using SPOCK (http://mackerel.tamu.edu/spock/) to create Raster3D script files for rendering with Raster3D (Merritt and Bacon, 1997). Molecular Cell 2004 16, 673-685DOI: (10.1016/j.molcel.2004.11.016)

Figure 3 Trimeric Major Coat Proteins (A) PRD1 P3 structure, (B) Bam35 P3 model, and (C) PBCV-1 Vp54. Ribbon diagrams show the side (in the plane of the virus capsid) and the top (from outside the virus along the molecular 3-fold) of each molecule. Each subunit has a separately colored ribbon with the jelly rolls in a lighter shade. Surface representations of the electrostatic potential provide top and bottom (from inside the virus) views. The electrostatic potential is displayed as shades of negative (red) or positive (blue) charge. Note that the bottoms of all three trimers are positively charged. Figures produced as described earlier. Molecular Cell 2004 16, 673-685DOI: (10.1016/j.molcel.2004.11.016)

Figure 4 Examples of Other Double-Barrel Trimers (A) A CLUSTAL X (Thompson et al., 1997) sequence alignment of PBCV-1 Vp54 (PBCV; GenBank accession number P30328) with the major coat proteins of Chilo iridescent virus (CIV; Q05815), African swine fever virus (ASFV; P22776), and mimivirus (MIMI). The MIMI major coat sequence was obtained from a search of ORFs of 300 or more amino acids by using SEQUINZ (http://www.ncbi.nlm.nih.gov/Sequin/index.html) from the National Center for Biotechnology Information (NCBI) on the 88 segments produced from whole genome shotgun sequencing of the mimivirus genome (GenBank accession numbers AABV01000001-AABV01000088). Conserved (black) and similar (gray) residues are boxed. The X-ray secondary structure of PBCV-1 Vp54 (Nandhagopal et al., 2002) is shown in the ALLSCRIPT (Barton, 1993) diagram above the sequence alignment (cylinders are α helices and arrows are β strands) and colored as in Figure 1C. (B–D) Models of the major coat proteins CIV P50, ASFV P72, and mimivirus. Residues that are inserted relative to PBCV-1 Vp54 are shown in yellow and the residues flanking deletions are in magenta. Selected loops are labeled. Molecular Cell 2004 16, 673-685DOI: (10.1016/j.molcel.2004.11.016)

Figure 5 Comparison of the Major Coat Proteins for Archaeal Virus STIV and Bacteriophage PRD1 (A) A CLUSTAL X (Thompson et al., 1997) sequence alignment of the corresponding major coat proteins (PRD1, GenBank accession number AAA32466 and STIV, AAS89101) with identical residues boxed in black and similar residues in gray. The secondary structure determined from the X-ray structure of PRD1 P3 is shown above the alignment with α helices represented by cylinders and β strands by arrows. The secondary elements involved in the jelly rolls are colored as in Figure 1A. (B) The STIV major coat protein model was made by threading its sequence onto the structure of PRD1 P3 (Benson et al., 2002) as described for Bam35 in Figure 2B but without energy minimization. Conserved (black) and similar (gray) residues are shown. Figures produced as described earlier. Molecular Cell 2004 16, 673-685DOI: (10.1016/j.molcel.2004.11.016)