Fig 1.
Structural comparison of the portal–tail complex in the P22 mature virion and the procapsid.
(A) Overall and cut-open views of the P22 mature virion (EMD-61453). The 100-Å scale bar applies to panels A and C. (B) Zoomed-in view of an atomic model of the portal–tail complex in the mature virion (PDB ID: 9JG6). (C) Overall and cut-open views of the P22 procapsid (EMD-61454). (D) Atomic model of the portal in the procapsid (PDB ID: 9JGA). (E) Ribbon model of the portal protein gp1 in the mature virion. (F) Ribbon model of the portal protein gp1 in the procapsid. (G) Structural comparison between the portal proteins in the procapsid and mature virion.
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.
Fig 3.
Structure of the SP complex and portal.
(A) Structure of the SP complex and portal within the capsid (EMD-61454). The capsid is not shown. A central windmill-like structure is highlighted in a red dashed box. Each side nodule, which contributes to a windmill blade, is marked with an asterisk. The remaining blades are marked with red dots. The structure of the SP-portal complex is tilted approximately 20°along the horizontal axis relative to that presented in Fig 2A. (B) Local reconstruction of the density map (transparent gray) of the SP tetramer at a resolution of 6.9 Å, superimposed on four copies of the gp8 models (magenta, cyan, green, and orange). The outermost part of each blade is contributed by the base domain (gray model superimposed) of a neighboring gp8 subunit (EMD-61456; PDB ID: 9KYX). (C) Local reconstruction of the top region of the dome, indicating that this region is also formed by the SP tetramers.
Fig 4.
Interactions among the SP, portal proteins, and major capsid proteins.
(A) Distribution of the hooks (red) on the inner surface of the capsid surrounding the portal (the portal is not shown) (PDB ID: 8I1V). (B) The portal and a copy of the inner base-associated SP are presented (PDB ID: 8I1V, 9KYW). Two of the 12 portal subunits interacting with the SP are indicated in green, whereas the remaining subunits are indicated in magenta. The color scheme for the SP domains matches that in Fig 2G. (C) Side view of panel (B). (D) Hydrophobic interactions between the portal protein (surface view) and the C-loop of the SP (ribbon view). (E) Models of the SP and portal protein superimposed onto the density map (EMD-61461; PDB ID: 9KYW).