To complement the homology model in Figure 1, the MV2-Eury DsrAB
heterotetramer was modeled also using AF2 Multimer (37). In this case
the Fe-S centers and siroheme moieties are not present in the modeled
structure. Three models were obtained, with the highest confidence
(highest pLDDT scores) found for model 3 (Figure 4, Figure S2). As can
be seen in the model colored according to the pLDDT score (Figure 4,
Figure S2), the only regions of the complex that were poorly predicted
in the models were in subunit A, residues 50-62 and 397-300. The first
region interacts with the DsrC subunit (Figure 1B), while the second
corresponds to four residues at the end of the first β-strand in a
β-sheet adjacent to the
A-subunit
ferredoxin domain. Alignment of the MV2-Eury AF2 model with the homology
model shows reasonable agreement (Figure 4), although the heterodimers
in the AF2 model are rotated with respect to each other around the
central axis of the heterodimer interface. Other notable differences are
the orientations of the side chains at central interface between
heterodimers (Figure S3) and a different orientation of the extended
C-terminal A subunit helices that contact the opposing subunits. Note
that the orientation of this helix is different in the A.
fulgidus and D. vulgaris structures as well. The region with the
low pLDDT scores (residues 50-62 in the A subunit) in the AF2 model
exhibits a similar configuration to that in the homology model (Figure
S3) but is rotated away from the center of the protein.