Help

Autophagy3D provides structural data for all 40 core autophagic proteins, their interactors and orthologs. Along with structures, the database provides metadata linked to each structure. The structures covered in the database include experimental structures and AlphaFold predicted models deposited in AlphaFold Database. The home page helps the user navigate to the core protein of interest. Upon clicking a protein, the website directs to the protein page where the user can access information about experimental structures belonging to the core protein, interactors and orthologs of the core protein. Users can also use the search bar by typing the core-autophagic protein of their interest.

Core Structure page: The first page contains different elements of information about the core autophagic protein.
General Information: This page provides key details related to the selected core protein. The first subsection of this page offers key details of the protein relevant to its role in the autophagy pathway. Also, related research articles are cited as PubMed IDs. Followed by general information, statistics on the experimental structures are provided.
Sequence space: The amino acid sequence (for human core autophagic protein) provided in the sequence space is interactive and connected to the structure visualization area. Upon clicking a residue in sequence space, the corresponding residue appears as a stick on the 3D structure.
List of available structures: Above the visualization area, the available experimental structures are listed and are available for download by clicking. The structures are sectioned based on biological assembly (monomer or a part of an oligomeric complex). Along with the experimental structures, users can also access the AF-predicted model.
Visualization space provides all the options to select and visualize the residues in different representations. Users can view the structures in full-screen and can also take a screenshot of the protein which will be saved as a PNG file. Along with the experimental structures, users can also access AF-predicted structures. In the visualization area, the AF-predicted structures can be coloured according to the pLDDT simply by clicking the ‘colour by pLDDT values’ box.

Interactome Page: Users can be directed to the interactome page by clicking ‘Interactors’ on top of the webpage. The interactor page has an interactive network coloured according to the structural availability. Users have the option to download the interactor metadata as a CSV file (by clicking the dialogue box given at the bottom of the interactive network).
Interactome sub-page: Upon clicking the node, a new tab opens a page where the information on the structural data of the interactor clicked is given. This sub-page majorly has the visualization space that has similar functionalities of the visualization in the core-proteome page. Below this, users can download the available experimental or AF-predicted structures.

Important Note: The interactor data are obtained from the BioGrid database which provides protein interactors whose interaction is validated by at least one experimental study. Although supported experimentally, these validations are mostly low-resolution cell biology or biochemical assays. This does not mean the physical complex of the core protein and its interactors have been captured through high-resolution structural biology techniques.

Ortholog Page: The last page provides the tabular information of the orthologs related to the core autophagic protein obtained from OrthoDB. Each preprocessed entry is annotated with the UniProt information. Users can download the metadata CSV file and AF-predicted structure coordinate files (compressed PDB files) for further analyses.

*Note: The protein description provided by OrthoDB is considered for preprocessing. The structures are AF-predicted models and are not experimentally determined.