Fig. 2: Structural organization of neck 1.

a Structure of neck 1 protein, gp14. The helical domain, β-sandwich domain, head joining (residues, 110–125) and lumen protrusion loops (residues 160–188) are colored dark pink, light pink, red and orange, respectively. b Superimposed view of all 12 protomers of gp14 in the Milano neck 1 ring, aligned at their helical-domain. The different conformations of β-sandwich domain and dual conformations of lumen protrusion loop are indicated by red and orange double-headed arrows, respectively. c Top view of neck 1 assembly in Milano. Color scheme is same as Fig. 2a. The β-sandwich domains are clustered asymmetrically in groups of three, four and five. The head joining loop of five protomers (n, n + 2, n + 5, n + 7, n + 10, CCW direction) are connected to MCPs at the 5-fold portal vertex, indicated by red circles. d Same view of Fig. 2c with capsid (grey), showing five out of twelve gp14 protomers (n, n + 2, n + 5, n + 7, n + 10, CCW direction) deviating from C12 symmetry to connect with the 5-fold capsid. e Interaction of the head joining loop of gp14 with MCP (gp9). The gp14 and gp9 subunits are shown as pink ribbon and cyan surface models, respectively. Cysteines involved in disulfide bonds are colored yellow and indicated by red dashed circles. f The lumen protrusion loop of gp14, by adopting a dual conformation, creates a two layered diaphragm-like structure in the lumen of the Milano neck. Two different layers created by different conformations are shown in pink and green.