FIGURE CAPTIONS
Figure 1. (A) Partial FoxB model obtained by experimental
phasing before the CASP14 model became available. At this point the
model could not be further improved and the project was stuck for a
year. (B) Experimental phases with partial FoxB model (map shown at 1.2σ
level).
Figure 2. Workflow of FoxB structure determination. The
structure was determined by MR-SAD using the AlphaFold2 model and
experimental phases. (A) Anomalous difference map with Se and Fe sites
at 2σ. (B) Overall map of FoxB after refinement (2σ). (C) Superposition
of the final model (green) and AlphaFold2 model (cyan) shows excellent
agreement. Density for heme groups (not present in AlphaFold2 model) is
shown.
Figure 3 . AlphaFold2 models of AR9 nvRNAP proteins fit the
cryo-EM density nearly perfectly. The cryo-EM-derived structures of
gp105, gp154, and two gp226 domains are colored according to the color
code given in the upper left corner of each panel. All AlphaFold2 models
are colored magenta. The electron density is contoured at 4.25 standard
deviations above the mean and colored semi-transparent grey. Regions
where no cryo-EM-derived structure existed prior to the availability of
the AlphaFold2 models are indicated with a dashed line and their
boundary residues are labeled.
Figure 4 . Inaccuracies in AlphaFold2 models. Cryo-EM-derived
structures and AlphaFold2 models of several AR9 nvRNAP subunits are
superimposed and regions where the conformation of the AlphaFold2 model
deviates significantly from the cryo-EM-derived structure are indicated
with a dashed line and their boundary residues are labeled. Note that
the folds of both the N- and C-terminal domains of gp226 were predicted
correctly, but the structure of the interdomain linker and the relative
orientation of the two domains were incorrect.
Figure 5. (A) The structure of TSP4-N homo-trimer with each
subunit in different color. The dash lines indicate structurally
disordered linkers between XD2 and XD3. (B) Superposition of XD2 as seen
in the crystal structure (magenta) and the structure predicted by group
427 (green) and group 226 (sky blue). (C) Superposition of AD crystal
structure (magenta) and the structure predicted by group 427 (green).
Figure 6. Polypeptide chain tracing errors that were corrected
by examination of the AlphaFold2 (group 427) structure. (A) The
incorrect model in the vicinity of two neighboring proline residues
(Pro236 and Pro239) together with the associated difference electron
density map with the coefficient 2Fo-Fccolored blue (left) and the model corrected based on the AlphaFold2
predicted structure with the associated
2Fo-Fc difference electron density map
(right). The cis bond conformations are highlighted in green (B) The
incorrect placement of Ile247 with the associated
2Fo-Fc difference electron density map
colored blue and the Fo-Fc difference
electron density map colored green (left). Correcting the positions of
Pro236 and Pro239 allowed placement of Tyr249 instead of Ile247 and
eliminated the residual Fo-Fc difference
electron density (right).
Figure 7. The crystal structure of dimeric Af1503 (grey) is
shown in a superposition with the best AlphaFold2 model (green,
monomer). The only noteworthy difference between the prediction and the
crystal structure is found in a loop in the PAS domain, which was found
to coordinate an ion in the crystal structure.
Figure 8. Superposition of Sia24 predictive and
crystallographic models. The structure of Sia24 (dark blue) was solved
with initial phase determination by molecular replacement using a model
generated by AlphaFold2 (yellow).