When executing a Sequence Quick Search, the iReceptor Gateway automatically sends a separate query to the Immune Epitope Database (IEDB) for this CDR3 via an Exact Search. If there is a successful hit - that is, if the query CDR3 sequence has known antigen specificity documented in IEDB – an informational box will appear underneath the CDR3 search box, displaying the relevant organisms. In this example, the CDR3 has known specificity to antigens from several organisms, including human and multiple types of viruses. To obtain more information on this epitope/antigen specificity, click on the IEDB link at the bottom of the box.
This link opens a new landing page at IEDB, which by default shows all available epitope records in the database (over 2M). There are different tabs to explore- Epitopes, Antigens, Assays, Receptors, and References from which each record was obtained. The left-hand panel provides options for filtering.
To perform a Receptor search, scroll down to the Receptor filter. Hover over the Receptor panel, and it will pop out. Enter your CDR3 sequence again (the same one you entered on the Gateway). You are essentially reproducing the search that the Gateway performed; in future, we hope to provide a direct link to the filtered search result page, but this is not currently possible.
Scroll down to the bottom of the page and click the Search button.
The filtered results now appear, as confirmed by the activated Receptor filter. As a sanity check, you may also confirm that the unique list of Organisms matches that provided by the Gateway.
Looking at the Receptors tab, we learn there are 145 records, all from T-cell receptors. The chain 2 (beta) CDR3 is the same for each record (it is the queried CDR3), while the chain 1 (alpha) CDR3 differs. Click on any receptor group ID (e.g. 820, the first one highlighted), and a new window will appear.
This provides an overview of the receptor record in IEDB, including gene usage, epitope/antigen specificity, experimental assays, and original references.