Figure 7
Mapping subunit interfaces and dynamics in large viral assembly- P4 hexamer within Ï•12 procapsid [94]. (A) Schematics of the viral procapsid (PC) and packaging of ssRNA precursors by the P4 hexamers associated with the capsid vertices (left). The right panel illustrates the problem of determining the orientation of the hexamer with respect to the procapsid. (B) Bar representation of the isotopic envelopes during progressive deuteration, free hexamer in red and PC-bound in blue. (C) The HDX kinetics derived from centroid positions of the isotopic envelopes in panel B (and from additional data not shown). (D) Mapping of average exchange rates onto P4 structure in surface color representation (color scale on the bottom right). (E) Fitting of the P4 hexamer into the EM-derived electron density using the correct orientation from HDX experiment (adopted from [113]). (F) Average exchange rates mapped onto the ribbon diagram of P4 subunit for free (left) and PC-bound (middle) hexamer together with the scaled crystallographic temperature factors (B-factors, right panel). Color scale as in panel D. (G) Schematics of ssRNA loading into the hexameric packaging motor via ring opening mechanism. Top: A specific viral RNA structure (packaging signal) is recognized by the major capsid protein P1 which brings the polynucleotide strand to the vicinity of P4. Middle: P4 ring opens and lets the RNA slip in between subunit interfaces into the central channel. Bottom: The ring topologically encloses the bound RNA and translocates RNA in 5' to 3' direction into the capsid at the expense of ATP hydrolysis (packaging).