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. Author manuscript; available in PMC: 2011 Mar 10.
Published in final edited form as: Structure. 2010 Mar 10;18(3):390–401. doi: 10.1016/j.str.2009.12.014

Figure 4. Sequence alignment and structure prediction of P22 coat protein.

Figure 4

The top two rows show secondary structure depictions of firstly, the final P22 CP model (yellow helices and cyan b-strands) as identified with the program Stride (Frishman and Argos, 1995) and secondly, as predicted (orange helices and violet b-strands) using the Jpred3 server (Cole et al., 2008). Next, the a.a. sequence of the P22 CP is listed above fifteen aligned sequences, which correspond to three different templates for HK97 gp5* (PDB ID: 1OHG), the CP of phage PfV virus-like particles (PDB ID: 2E0Z), bacteriophage T4 gp24 (PDB ID: 1YUE), hypothetical prophage proteins from B. bronchiseptica (PDB ID: 3BQW) and E. coli (PDB ID: 3BJQ), the encapsulin from T. maritima (PDB ID: 3DKT) (Pei et al., 2008), three templates of the D1 and one of the D2 domain of the human Fc receptor (PDB ID: 1E4J), telokin (PDB ID: 1FHG), and the D1 and D2 domains of human Ig Epsilon (PDB ID: 1F2Q). Alignments produced using the FFAS03 (Jaroszewski et al., 2005) and PROMALS3D (Pei et al., 2008) servers are labeled accordingly. Alignments for HK97 gp5* (Template), Ig Fc receptor D1 (Template), and telokin were adjusted manually using the described iterated procedure. Regions corresponding to the HK97 and telokin folds are shaded in green and pink, respectively. The area shaded in white corresponds to the unmodeled portion of the CP, and the region shaded in yellow corresponds to the 2-strand β-strand insert modeled from the hypothetical prophage protein. Sequence shading is based on the Jalview Blosum62 coloring. Briefly, the residue is colored dark blue (HK97) or dark purple (telokin) if it matches the consensus sequence (not shown) (Clamp et al., 2004).The residue is colored light blue (HK97) or light purple (telokin) if it does not match the consensus sequence, but has a positive Blosum62 score (Clamp et al., 2004). Colored circles beneath the aligned sequences identify residues 170 (blue), 285 (green), and 379 (red), where nanogold-labeling occurred in P22 shell variants studied by cryo-TEM. Regions of the CP identified by trypsin digestion are highlighted with yellow and pink bars, corresponding to the N-terminal arm and telokin domain, respectively.