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. 2022 May 30;25(7):104496. doi: 10.1016/j.isci.2022.104496

Figure 2.

Figure 2

Modeling of Epsilon15 gp7

(A) The structure of a single gp7 subunit (PDB: 3J40_B) is shown. The model is colored from the N-terminus (blue) to the C-terminus (red). The N-terminus is enclosed by a dashed box, the long β-sheet is enclosed by a dashed triangle, the internal β-sheet is shown enclosed by a dashed circle, and the large hexonal loop is marked with an arrow.

(B) The AlphaFold2 model for gp7 is shown as a ribbon colored by the pLDDT value.

(C) The AlphaFold2 model for gp7 after real-space refinement in Phenix is shown superimposed on the density map for a single gp7 subunit and colored based on B-factor.

(D) The final model for gp7 based on the AlphaFold2 prediction and refined against the density with Phenix and Coot is shown. The model is colored by RMSD, comparing it with the published structure, 3J40_B.