In Situ Structures of the Ultra-Long Extended and Contracted Tail of Myoviridae Phage P1

Abstract

The Myoviridae phage tail is a common component of contractile injection systems (CISs), essential for exerting contractile function and facilitating membrane penetration of the inner tail tube. The near-atomic resolution structures of the Myoviridae tail have been extensively studied, but the dynamic conformational changes before and after contraction and the associated molecular mechanism are still unclear. Here, we present the extended and contracted intact tail-structures of Myoviridae phage P1 by cryo-EM. The ultra-long tail of P1, 2450 Å in length, consists of a neck, a tail terminator, 53 repeated tail sheath rings, 53 repeated tube rings, and a baseplate. The sheath of the contracted tail shrinks by approximately 55%, resulting in the separation of the inner rigid tail tube from the sheath. The extended and contracted tails were further resolved by local reconstruction at 3.3 Å and 3.9 Å resolutions, respectively, allowing us to build the atomic models of the tail terminator protein gp24, the tube protein BplB, and the sheath protein gp22 for the extended tail, and of the sheath protein gp22 for the contracted tail. Our atomic models reveal the complex interaction network in the ultra-long Myoviridae tail and the novel conformational changes of the tail sheath between extended and contracted states. Our structures provide insights into the contraction and stabilization mechanisms of the Myoviridae tail.

Keywords: bacteriophage P1; cryo-EM; tail contraction mechanism; tail sheath protein; ultra-long tail.

Figure 1

Cryo-EM image, overall structure and protein density maps of the phage P1. (A) Cryo-EM image of phage P1 showing the extended and contracted states. The contracted tails are marked by white triangles. (B) An intact extended P1 particle image showing the long and straight tail. (C) An intact contracted P1 particle image showing the contracted tail sheath and the exposed tail tube. (D) Surface view of the intact extended tail of P1. The lengths of the intact tail and tail trunk are labeled. The tail trunk consists of fifty-three rings, and the first and fifty-third rings are labeled L1 and L53, respectively. (E) Local reconstruction of the extended tail corresponding to the dashed box in panel (A) at 3.3 Å. Left: One of the six subunits of each sheath ring is presented in magenta to depict the helix assembly of the tail sheath. Right: Half of the tail sheath is removed to show the tail tube, and one of the six subunits of each tube ring is presented in yellow. (F–H) Extended density maps (gray) of the tail terminator protein gp24 (F), the tail tube protein BplB (G), and the tail sheath protein gp22 (H) superimposed on their atomic model (ribbon). The atomic models are shown in rainbow colors, ranging from blue at the N-terminus to red at the C-terminus, and the N-terminus and C-terminus of gp22 are labeled. (I) Surface view of the contracted intact tail of P1, showing that the tail sheath shrinks to 940 Å and the tail tube is exposed to the outside. (J) Local reconstruction of the contracted tail corresponding to the dashed box in panel (I) at 3.9 Å. The color codes are identical to panel (E) to show the helix assembly of the contracted tail sheath. (K) Contracted density maps (gray) of the tail sheath protein gp22 superimposed on the atomic model (ribbon). The viewing direction is identical to panel (H), and the N- and C-terminus of gp22 are labeled to show the conformational changes between the extended and contracted states.

Figure 2

Structure of the P1 tail terminator. (A) The cryo-EM maps showing the interfaces between the tail terminator and the tail tube/sheath. (B,C) Side and top views of the tail terminator ring. One of the six gp24 monomers is shown in rainbow colors, ranging from blue at the N-terminus to red at the C-terminus. (D) Ribbon model of gp24 with the four domains labeled. (E–G) Superpositions of protein gp24 of P1 on the terminator protein of T4 (PDB ID: 3J2N), the cap protein of Algo (PDB ID:7adz) and the collar protein of R2 pyocin (PDB ID: 6u5j). The color code of gp24 is identical to that in panel (D).

Figure 3

Structure of the P1 tail tube. (A) The cryo-EM map showing the interfaces between the tail terminator and tail tube. The tail sheath is removed to show the tail tube, and one of the six BplB monomers in each tube ring is colored yellow to show the helix assembly of the tail tube. (B) Side (left) and top (right) views of a tail tube ring. The inner and outer diameter of the ring are labeled. One of the six BplB monomers is shown in rainbow colors, ranging from blue at the N-terminus to red at the C-terminus. (C) Atomic model (ribbon) of the tail tube protein BplB. (D) Atomic model (ribbon) showing the interactions between two adjacent tube rings. (E) Electrostatic potential surfaces of the interactions between two adjacent tube rings. (F) The electrostatic potential surface of the inner tail tube. (G) Conformational changes of the tail tube protein BplB between layer 53 and other layers. (H) β-sheet augmentation interaction between the N-terminus of the tube protein BplB and the β-hairpin domain of the terminator protein gp24.

Figure 4

Structure of the extended tail sheath of P1. (A) Cryo-EM map of the tail, including the hexameric terminator (cyan), three (L51, L52, and L53) hexameric sheath rings (gray) and tube rings (yellow). The adjacent three gp22 monomers are colored in magenta, green, and orange, and the N-terminus and C-terminus of the three gp22 monomers and one gp24 monomer are colored in blue and red, respectively, to highlight the interactions. (B) Ribbon model showing six handshake interactions between N-terminus (blue) and C-terminus (red) in a sheath ring. The inner diameter of the sheath is labeled. (C) Ribbon model of the protein gp22. (D) Zoom-in view of the blue box in panel (B) to show the electrostatic interactions between the tail tube and sheath. (E) β-sheet augmentation interactions between two adjacent sheath rings. (F) β-sheet augmentation interactions between the 53rd sheath ring and the terminator. (G) Model superposition to show the conformational changes of the proteins gp22 in the 53rd and other layers.

Figure 5

Conformational changes of the contracted P1 tail sheath. (A) Cryo-EM map of the three sheath rings of the contracted tail. The color codes are identical to those of Figure 4A. (B) Ribbon model showing six handshake interactions between N-terminus (blue) and C-terminus (red) in a contracted sheath ring. The inner diameter of the sheath is labeled. (C) Model superposition to show the conformational changes of the sheath proteins gp22 between extended and contracted states. (D) β-sheet augmentation interactions between two adjacent contracted sheath rings.