What is ABC3D?

Our web application, was developed to provide a thorough collection of available experimental and computational structures of ABC proteins in an organized manner. Our database is updated regularly, PDB and AlphaFold databases are checked weekly for new structures.

What are ABC proteins?

ABC (ATP Binding Cassette) proteins play crucial roles in diverse biological functions from bacteria to man. The functional form of an ABC protein includes two NBDs (nucleotide binding domains) and two TMDs (transmembrane domains). These domains can be encoded in one chain in the case of full transporters and in two or more chains in the case of multimeric forms.

ABC proteins can be observed in various conformations. Generally, in the absence of bound ATP to NBDs, ABC proteins exhibit an "open", inward-facing conformation towards the intracellular space, capable of substrate binding. When two ATP molecules are bound, the NBDs close and form a tight interaction and the extracellular ends of TM helices may open to provide a dissociation site towards the extracellular space (outward-facing conformation).

How do you screen existing databases for ABC protein structures?

We used selected Pfam entries matching NBDs and TMDs of ABC transporters. These entries can be downloaded from here.

What are Pgp-like, ABCG2-like and other -like categories in the website?

We classified the collected structures based on their heterogeneous and non-conserved TM domains similar to the work of Thomas et al. Instead of the usual, numbered structural classes we use names related to a well-known representative member of a class (hence the names Pgp-like, ABCG2-like and so on).

What are open/closed groups on the website?

Since ABC protein structures usually can be observed in two characteristic functional conformations, we found it important to also categorize our proteins based on these states. Open: NBDs are not tightly closed and the structure is inward-facing in most of these cases. Closed: the NBDs are tightly closed in the presence of nucleotides and the structure is sometimes outward-facing. To determine their conformational states, we used a method based on special geometric measures, conftors.

How can I select a specific structure or multiple structures manually?

Select the structural subgroup of your target protein and click on it. A drop-down list will appear with two options: open or closed. Please select your desired conformational class and click on it. Another drop down list will appear with the protein structures of the selected structural family and conformation. Each row represents a protein structure, and contains information about the PDB or AFDB ID, corresponding gene(s) and species of the protein structure. Towards the end of the row, you can click on the eye button to visualize the structure in Mol* to the right. At the end of the row, you can find links pointing to either AFDB (in case of most computational structures), PDB and PDBe (in case of experimental structures) or the 3D-Beacons client of Hegelab, in case of our AF2-built homodimeric ABC structures. You can scroll down the drop down list to find more structures. If you've found the structure you were looking for, simply tick the box at the beginning of its corresponding row and click on the gray Download button at the top of the list. You can select multiple structures with this method and Download them at once.

Can I search for a protein structure by name, gene or species?

On top of the drop-down lists, you can see a blue 'Select' buttton. Click on it to perform more advanced search queries. You can select the conformation, structural family and the broad type of species you are looking for (e.g. unicellular, vertebrate, etc). You can also filter for the release date of the structure. There is also a text box where you can type keywords and if it matches a structure, it will be selected. For example, if you type in "zebrafish cftr", a search is performed in every row and rows where both zebrafish and cftr are present in either cell, will be selected.

How can I select multiple structures at once?

If you wish to select all structures found in a structural family or in a conformational subgroup of a structural family, you can select them by clicking on the green 'Select' button at the top of the drop-down list. You can also select multiple families this way, by clicking on their name and selecting them with their corresponding green select button. You can always control how many structures you have selected from a structural family by checking the numbers next to their names. The number in the grey box is static, it shows the amount of all structures present in the family. The number in the cyan box shows how many structures are selected at the moment from said family.

You can also visit the Download page to find zip files containing all structures of structural families in pdb and cif formats.

How can I download or select every structure of one specific structural family?

You can select them manually by clicking on the green Select button at the top of the drop-down list. For a more convenient option, you can visit the Download page and browse through the prearranged zip files containing every member of a structural family in pdb and cif formats.

How can I visualize structures before download?

Find the structure by opening the correct drop-down lists and click on the eye icon in the corresponding row to visualize it on the right side of the webpage using Mol*.

What file formats are available through your website for download?

You can download selected structures in pdb format or you can visit the Download page to download a whole subgroup of structures in both pdb and cif format.

Please keep in mind that when using manual selection, the Download button will open a small pop up window in the same page and you should select whether you would like to download only the metadata of selected structures (in .tsv format) or the structures as well. After clicking Download, please wait a few seconds and check the status of download in your browser. if your download is complete, please close the small pop-up window as it will not disappear on its own, and you can continue browsing our website.

How can I select only experimental or computational structures?

At the end of each row, you will find a small symbol representing either PDB or AF2, indicating whether a structure is experimental or computational, respectively. Also, you can select "Experimental" or "Computational" items from the main navigation bar. This way you will be taken to a page with only experimentally or computationally solved structures.

Can I select human ABC protein structures based on their usual classification(ABCA, ABCB, etc.)?

Yes, we included human ABC structures based on their commonly used classification. All known human structures can be classified into two structural classes: (1) ABCA and ABCG proteins belong to the ABCG2-like family, (2) while ABCB, ABCC and ABCD families exhibit Pgp-like structures.