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![[Figure 3]](jb5042fig3mag.jpg)
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Figure 3
Comparison of unexpected PDZ conformation features with predicted structures. (a) Superposition of the experimental structure (green) and AlphaFold prediction (pink) of the PDZD7_3 PDZ domain. An enlarged view is shown focused on the extended α2 helix and on the PBM binding pocket. (b) Manual AlphaFold predictions (n = 5) of the PDZD7_3 PDZ domain bound to the PBM of EXOC4. The C-terminus of the PBM lies farther than optimal from the carboxylate-binding loop of the PDZ domain. (c) Superposition of the experimental structure (cyan) and AlphaFold prediction (pink) of the SNTG1 PDZ domain. An enlarged view is shown focusing on the α1 helix. The figure was prepared using the structure of SNTG1 bound to the PBM of TRPV3. The structures of both PDZD7_3 and SNTG1 were solved after the AlphaFold predictor had been trained. While the predicted structure lies very close to the experimental structure in the case of PDZD7_3, it is more divergent in the case of SNTG1. The final 2Fo − Fc electron-density map is shown at 1σ in both panels. (d) Manual AlphaFold predictions (n = 5) of the SNTG1 PDZ domain. All predictions adopted highly similar conformations with the α1 helix in the conventional conformation. Predictions do not provide indications for structural variability in this region. |
![[Figure 3]](jb5042fig3.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
