Fig 6. Simplest arrangement satisfying topological restraints between structural proteins p4a, p4b, A4, and F17.

‘N’, ‘C’, ‘F1’, ‘F3’, ‘F2’ refer, respectively, to protein N- and C-termini, proteolytic fragments 1 and 3 of p4a and fragment 2 of p4b. p4a-fragment 2 and p4b-fragment 1 have been discarded. Pink trapezoids: The p4a/p4b and p4a/A4 interaction regions (from Fig 5a). Pink wedge: The F17(K74)/p4a interaction region (from Fig 5d). Broken red lines: XL from F17(K74) to both ends of protein A4 (from S1 Fig). The arrangement shown also emphasizes the absence of p4b interaction with either A4 or F17 and the absence of any interactions within the four-protein complex of protein A4’s C-terminal half or p4a’s N-terminal region (Fig 5a and 5d). Also accounted for are the three-domain structure of protein A4 (Fig 5c) and a core-wall exterior location for A4 as predicted by immunoEM studies ([7, 8]). Among the membrane proteins, interaction sites for J5, A21, H3, A16, G3, A26 and ATI cluster at the C-terminal region of p4a (yellow line) while A17 interacts further upstream, with p4a fragment 1 (yellow circle; from S1 Fig). p4b’s only interaction with a bona fide membrane protein is with A17 (yellow circle; from S1 Fig). This membrane protein arrangement suggests that p4b may be oriented towards the interior of the core. Green lines: Regions of structural proteins that interact with transcriptosome components (from S1 Fig). These presumably extend into the third dimension.