Fig. 6: TraI conformational changes, requirement for bubble formation 3’ of nic.

a TraI conformational changes. TraI TE, VH and AH domains are shown in surface representation, colour-coded orange, green and violet and labelled correspondingly. Top: TraI’s helicase mode (TraI_helicase). Bottom: TraI’s TE mode (TraI_TE). See main text for definition of TraI_TE and TraI_helicase. b TraI VH domain in the relaxosome (TraI_TE at left) versus in TraI_helicase (right). VH_NTD, VH_1A and VH_{2A+2B/2B-like} are shown in dark green, olive and green surface, respectively. In TraI_TE, VH_NTD and VH_{2A+2B/2B-like} is found rotated by 47° and 95° relative to VH_1A, respectively. c The TE domain of ds_{-27_+143}-R structure is flexibly positioned but locates in a region similar to that of the TE domain of ss_{-27_+8}ds_{+9_+143}-R. Two 2D-classes in the same orientation are shown, one for ds_{-27_+143}-R (left) and one for ss_{-27_+8}ds_{+9_+143}-R. Left: a “fuzzy” density in shown in dash-lined orange circle. Right: the TE and DNA of ss_{-27_+8}ds_{+9_+143}-R is mapped on the 2D-class in such a way that its DNA is placed on top of the DNA’s 2D-projection. This positions the TE in the density shown at left, demonstrating that this density is generated by the ds_{-27_+143}-R TE domain. However, the density is “fuzzy”, indicating the domain is flexibly located. Thus, TraI in ds_{-27_+143}-R is likely similarly positioned as in TraI_TE.