Alphafold predicted structures of VPS13 proteins from model organisms

This upload contains AlphaFold-predicted structures of VPS13 proteins from a variety of organisms. Given the large size of these proteins, only partial sequences were predicted with AlphaFold(1) and the resulting structures were aligned in PyMOL(2). A summary of the structures uploaded here is presented as a collection of domain cartoons in the "VPS13 domain organization across eukaryotic evolution.pdf" file. 

The structures were generated with AlphaFold v2.029 on the Yale High Performance Cluster. Each *.zip file contains the best ranked predictions (out of five) for each sequence (*.pdb files) and the PyMOL assembled full structure (*.pse file). In a few cases, where a good alignment was not possible due to long disordered regions in the C-terminal portions (mostly in proteins from D. discoideum and A. thaliana), the full structures were aligned manually in PyMOL based on the continuity of the lipid transfer groove. The structures in PyMOL can be colour-coded by the confidence value of AlphaFold predictions using the following prompt:

set_color n0, [0.051, 0.341, 0.827]
set_color n1, [0.416, 0.796, 0.945]
set_color n2, [0.996, 0.851, 0.212]
set_color n3, [0.992, 0.490, 0.302]
color n0, b < 100; color n1, b < 90
color n2, b < 70;  color n3, b < 50

Considering that full length structures were assembled by aligning different protein fragments and in view of the presence of flexible loops with low prediction confidence scores, the relative positions of different folded domains are not necessarily correct.

References

1. J. Jumper, et al., Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

2. The PyMOL Molecular Graphics System, Version 2.0. Schrödinger LLC.