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 <em>D. discoideum</em> and <em>A. thaliana</em>), 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]<br> set_color n1, [0.416, 0.796, 0.945]<br> set_color n2, [0.996, 0.851, 0.212]<br> set_color n3, [0.992, 0.490, 0.302]<br> color n0, b &lt; 100; color n1, b &lt; 90<br> color n2, b &lt; 70; color n3, b &lt; 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. <strong>References</strong> 1. J. Jumper, <em>et al.</em>, Highly accurate protein structure prediction with AlphaFold. <em>Nature</em> 596, 583–589 (2021). 2. The PyMOL Molecular Graphics System, Version 2.0. Schrödinger LLC.本上传数据集包含多种生物体的VPS13蛋白的AlphaFold（AlphaFold）预测结构。鉴于此类蛋白分子尺寸庞大，仅部分序列通过AlphaFold(1)完成了预测，所得结构已通过PyMOL(2)进行对齐。本次上传的结构汇总信息以结构域卡通图集的形式收录于"VPS13 domain organization across eukaryotic evolution.pdf"文件中。这些结构是在耶鲁大学高性能计算集群上使用AlphaFold v2.029生成的。每个*.zip文件包含对应序列的5个预测结果中排名最优的预测结果（*.pdb格式文件），以及经PyMOL组装得到的完整结构文件（*.pse格式文件）。少数情况下，由于C端区域存在较长无序区段（多见于<em>D. discoideum</em>和<em>A. thaliana</em>的蛋白），无法完成有效对齐，此时研究人员基于脂质转运沟的连续性，在PyMOL中手动完成了完整结构的对齐。在PyMOL中可通过以下命令，根据AlphaFold预测的置信值对结构进行颜色编码：<br>set_color n0, [0.051, 0.341, 0.827<br>set_color n1, [0.416, 0.796, 0.945<br>set_color n2, [0.996, 0.851, 0.212<br>set_color n3, [0.992, 0.490, 0.302<br>color n0, b &lt; 100; color n1, b &lt; 90<br>color n2, b &lt; 70; color n3, b &lt; 50<br>考虑到完整全长结构是通过对齐不同蛋白片段组装而来，且存在预测置信度较低的柔性环区域，不同折叠结构域的相对位置未必准确。<strong>参考文献</strong><br>1. J. Jumper等，基于AlphaFold的高精度蛋白质结构预测。《自然》（*Nature*）596, 583–589 (2021)。<br>2. 《PyMOL分子图形系统，版本2.0》。Schrödinger LLC。