Fig 1.
Structures of myophage P1 with three states, including the extended P1, the contracted P1 with partial DNA and the contracted P1 without DNA.
(A) Representative cryo-EM images of the three states of P1. The icosahedral vertices of the contracted P1 without DNA were boxed. (B) Side (left), cut-open with manually removed DNA (middle) and cut-open (right) views of the intact structure of extended P1. L1 and L53 denote the first and final layers of the tail sheath, respectively. The inset shows the central cross-section of the head-connector in the extended P1. (C) Zoomed-in view of the inner surface around an icosahedral vertex to show the interactions among DarA, Hdf, DNA, a mass of low-resolution density (the unkonwn protein) and capsid in the extended P1. (D) Zoomed-in view of density maps (transparency) of Dar proteins and DNA in the extended P1 superimposed on its atomic models. The atomic models of the α-helix domain of DarA (cyan) and Hdf (lime) were manually built. The atomic models of the hexon and penton binding domains (magenta) of DarA were obtained by manual building and AlphaFold3 combination. The atomic models of Hdf N-terminus (light green) and DNA (yellow) were directly generated by AlphaFold3. (E) Cut-open view of the intact structure of the contracted P1 with partial DNA. The inset shows the central cross-section of the head-connector in the contracted P1 with partial DNA. (F) Zoomed-in view of the inner surface around an icosahedral vertex to show the interactions among DarA, Hdf, DNA, and capsid in the contracted P1 with partial DNA. (G) Zoomed-in view of density maps (transparency) of Dar proteins and DNA in the contracted P1 with partial DNA superimposed on its atomic models. The color codes are identical to that in Fig 1D. (H) Zoomed-in view of the inner surface around an icosahedral vertex in the contracted P1 without DNA, DarA and Hdf extracted from the red box in panel A. (I) Organization of P1 genome segment. The color codes are applied to panels B-H.
Fig 2.
Structures of the major capsid protein gp23 of P1.
(A) Ribbon model of the MCP gp23 shown in five domains. (B) Ribbon model of an asymmetric unit of the icosahedral capsid. Color codes are identical to that used in Fig 1B. (C) Top view of the capsomeric interactions along the three-fold and quasi-three-fold axis. One penton and two hexons are colored orange, green, and light sea green, respectively, except for an MCP colored in medium purple. The I-domains of all MCPs are colored magenta. (D-F, H and I) Zoomed-in views of the box regions in panel C to show the interactions in the intra- and inter-capsomeres, including hydrogen bonds and salt bridges (D, E and I), β-sheet augmentation (F), and hydrophobic pocket (H). (G) Structural comparison of the centers of penton (left) and hexon (right).
Fig 3.
Structures of the Hdf and DarA in P1.
(A) Interactions between Dar proteins, DNA, and capsid. Color codes are identical to that used in Fig 1B, except for Hdf and DarA colored according to their domains. The color code is applied to panels A-E. (B) Ribbon model of the Dar proteins, colored according to their domains. The N-terminus of Hdf is predicted by AlphaFold3. (C) Zoomed-in views of the interactions among the capsid and the α-helical domains of DarA and Hdf. (D) Electrostatic potential surfaces of α-helical domains between Hdf and DarA. (E) Interactions among DNA and N-terminal domain of Hdf and DarA. (F, G) Positively charged inner surface (F) and hydrophilic outer surface (G) of the N-terminal domain of Hdf and DarA.
Fig 4.
Structures of the connector complex of the extended P1.
(A, B and C) Cut-open (A), side (B) and top (C) views of the connector complex of the P1. Color codes are identical to that used in Fig 1B. The top inset shows a zoomed-in view of the interactions between an adaptor monomer and two adjacent portal monomers, forming a four-stranded β-sheet. The bottom inset shows a zoomed-in view of the α-helix domain of the stopper capping the α-helix bundle domain of the adaptor by forming a huge hydrophobic pocket. (D, E and F) Ribbon models of the portal protein Prt (D), the adaptor protein PmgC (E) and the stopper protein gp7 (F), colored according to their domains.
Fig 5.
Structures of the simple baseplate in extended P1.
(A) Side (left) and cut-open (right) views of the ribbon models of the simple baseplate. The top inset shows a zoomed-in view of the interaction between a BW1 monomer and two adjacent sheath monomers, forming a four-stranded β-sheet. The bottom inset shows a zoomed-in view of the interactions among plug, hub and wedge. The color coding is identical to that used in Fig 1B. The tripod and fibers are shown in density maps. (B) Ribbon model of the center region of the baseplate. (C-F and I) Ribbon models of the tube initiator Tub (C), tube-linking PmgG (D), hub gp6 (E), spike UpfC (F) and plug gp26 (I). The hub protein gp6 is colored according to its domains. (G) Ribbon models of BW1, BW2, BW3-i and BW3-o in the heterotetrameric wedge. (H) The bottom view of the ribbon model of the six-fold symmetric wedge.