Extended Data Fig. 5. Generating the composite T4SS model shown in Fig. 1d.

a, Derivation of the C6 symmetry operators. The same particles used to generate the Ab Initio model for the IMC, Arches, and Stalk (Extended Data Fig. 2c) were used to generate an Ab Initio model with C6 symmetry imposed. The resulting map was used to generate the C6 symmetry operators using PHENIX. b, Positioning the OMCC relative to the IMC, Arches, and Stalk. As explained in Methods, the same C6 map was used to position the I-layer part of the OMCC. c, Verifying the positioning of the OMCC relative to the IMC, Arches and Stalk. While in most 2D classes, the OMCC is not aligned with the IMC-Arches-Stalk, in about 2.4 % of the particles, it is. Using these 2D classes, the distance (reported here) between the Arches and the I-layer was used to check that the positioning of the OMCC relative to the rest of the structure is correct.