Fig. 5: Structure of the assembled phage.

Pentameric layers of pVIII are coloured differently according to their position in the filament e.g. layer r1 in light blue is the first layer at the round (r) tip, and layer p7 in bright green is the 7th layer at the pointy (p) tip. pVII is shown in pink and pIX in yellow. Hydrogen bonds within the different layers are shown with blue dashed lines. a Five copies of alternating pIX and pVIII line the outside of the pVII bundle at the round tip. In layer 1, interactions are mainly hydrophobic, with salt bridges between pIX and pVII (Glu 29 to Arg 33), and hydrogen bonds between pIX and pVIII (Thr 30 to Lys 43, and Glu 29 to Lys 40). In layers 2–3, pVIII interacts with pIX and neighbouring pVIII molecules via hydrophobic interactions. The pVIII in layer 4 onwards interacts with other pVIII molecules only, via hydrophobic interactions and with inter-subunit hydrogen bonds between Lys 43 and Lys 48, and Ser 47 and Lys 40. b Layers of pVIII interact with 5 copies of pIII and pVI at the pointy tip. In layer 1, pVIII interacts with pIII, pVI and neighbouring pVIII molecules, forming hydrogen bonds between Tyr 24 and Lys 363 of pIII, and between Lys 44 and Ser 50 of a neighbouring pVIII from layer 2. In layer 2, pVIII forms hydrogen bonds from Lys 43 to Lys 48 of neighbouring pVIII molecules from layer 3. In layer 4 onwards, pVIII interacts with other pVIII molecules only, with hydrogen bonds between Lys 43 and Lys 48 from adjacent layers. c Composite models of the f1-derived nanorod and WT f1 phage were generated by aligning the tips with multiple copies of the pVIII filament protein and an AlphaFold model of the linkers and N1-N2 domains of pIII. pVII is shown in pink, pIX in yellow, pIII in orange, pVI in purple and pVIII in light blue. A view rotated 90° depicts four of the N1-N2 domains of pIII in orange and one coloured differently to highlight the N1 domain (teal) and N2 domain (light pink).