Structure of the scaffolding protein and portal within the bacteriophage P22 procapsid provides insights into the self-assembly process
Fig 2
Structure of the P22 procapsid.
(A) Structures of the SP complex (cyan) and portal (magenta) within the procapsid (EMD-61454). The front half of the capsid is not shown. The SP hook domains anchored to the inner capsid surface are indicated in red. (B) Cut-open view of the SP complex. (C) Slab-view of the red box from the top in panel (B). Each side nodule is marked with an asterisk. The nine nodules on the portal are numbered. (D) Slab-view of the green box from the top in panel (B). The nodules on the portal are numbered. (E) SP complex and portal viewed from the left side of panel (C). Each column is marked with a triangle. Each side nodule is marked with an asterisk. The nodules on the portal are numbered. (F) Local reconstruction of the density map in the blue box in panel €. The side nodule in the middle is removed for clarity. The density map is superimposed on three SP models (EMD-61455; PDB ID: 9KYY). (G) Ribbon view of the AlphaFold2-predicted SP model, with SP domains in different colors. (H) Zoomed-in view of a nodule density map superimposed on two copies of the base domains of the predicted SP model (EMD-61452; PDB ID: 9KYV). (I) Left: atomic model of the portal (magenta) and the nodules (PDB ID: 9KYV, 9JGA). The inner SP base domains are in cyan, and the outer base domains are in orange. Right: a slab-view of the left view. (J) Zoomed-in view of a nodule density map superimposed on two copies of the base domains of the predicted SP model (PDB ID: 9KYV). The color scheme of the models is identical to that in panel (I). (K) Schematic of panel (E). The four nodules (group of 4) are numbered 1–4. Each nodule is formed by a dimer of the SP base domain. Each column (marked with a red triangle) is a three-helix bundle (three SP column domains). The side nodules (base dimer) are marked with asterisks.