The IEDB catalogs T cell receptor (TCR) and B cell receptor (BCR/antibody) sequence data with experimentally verified epitope specificities from published literature. Receptor data can be directly queried from the homepage, and results are displayed in their own ‘Receptors’ tab.
When using the IEDB receptor data, please cite our preprint: “Revised Adaptive Immune Receptor Data in the Immune Epitope Database”. This preprint provides a detailed description of how curated receptor data was standardized for the database.
The following information is provided for each receptor, if available:
- Full-length nucleotide or amino acid sequence as provided by the original source, alongside with their GenBank accession identifiers.
- V domain amino acid sequence, which corresponds to the computationally standardized V-D-J or V-J region, and may be shorter than the full-length sequence.
- CDR1, 2, 3 and Junction sequences. The CDR3 and Junction sequences represent the same region, but the CDR3 is reported excluding the conserved starting conserved Cys104 and Phe/Trp118 residues, whereas the Junction includes them. CDRs are annotated from full sequence if available, or curated from literature.
- V, D and J gene annotations. Gene names are annotated from the full sequence if available, or curated from literature.
- Receptor type and chain types (e.g., TCR with α and β chains), and the organism which the receptor originates from.
- Linked information from all other IEDB data tables, such as the recognized epitopes and their antigen origin, experimental assays, including the assay type (tetramers, x-ray crystallography), assay outcomes (binding/nonbinding), the MHC restriction for T cells, the reference to the source publication, and more.
Receptor Results Tab
The Receptors tab is split into two sub-tabs for T and B Cell Receptors. The data is presented in a table showing the Receptor Group ID, the Species the receptor originated from, the receptor Type, the CDR3 of each chain and cognate Epitope. The chains are presented in the order of the receptor type, e,g., for αβ TCRs, Chain 1 is the α chain, and Chain 2 is the β chain.
These tables show a quick overview of the data. More detailed information can be found by clicking the Group ID which brings you to the Receptor Details Page, or by Exporting Results. Since this table shows receptor–epitope pairs, the receptors that are associated with multiple distinct epitopes are duplicated, such as Receptor Group 49 in the example below.
Receptor Groups and the Receptor Details Page
Multiple different experiments may describe the same immune receptor, binding to either the same or different epitopes. To deal with duplicate receptor data, the IEDB organizes receptors into Receptor Groups, which are characterized by their receptor type, CDR3 sequence(s) and organism, and are presumed to have the same specificity.
The Receptor Details Page shows a summary of the data for a given Receptor Group. The first block contains a summary of the grouping information, as well as links to accession identifiers. Next, a table summarizes all available information for each individual receptor belonging to the group: gene usage, CDR sequences and V domain sequence, as well as the associated epitope(s). Note that since the CDR3 sequence(s) are the only sequence information that define a receptor group, these receptors may have different CDR1/2 or V domain sequences, or V/D/J gene annotations. For instance, the example below shows a receptor group with different beta chain CDR2 sequences and V domains. Lastly, the epitope summary provides links to every epitope, assay and publication associated with this receptor group.
To export data from the Receptor Details Page, click the receptor Group ID in the title, which will bring you back to the Receptor Results Tab filtered for this receptor group. From there, the data can be exported by clicking Export Results. When exporting receptor data, ‘IEDB Receptor ID’ refers to the individual receptors, and ‘Group IRI’ contains the group identifier, which links back to the Receptor Details Page. To omit potential duplicate data, one representative receptor may be retained per receptor group–epitope pair.
Querying for Receptor Data
Homepage Query
From the homepage, receptor data can be queried directly using the Receptor (TCR/BCR) search box. By selecting the ‘Has sequence - TCR / BCR’ checkboxes, the search results are limited to only include data from assays where information about the immune receptor was characterized. Because the IEDB contains broad epitope data, including from epitopes where the exact receptor was not known, we recommend users interested in receptor data to check these boxes.
For users who are interested in checking if a specific receptor has been described in the IEDB, the chain (alpha/beta/heavy/light etc) or CDR3 sequence may be specified in the homepage search box. The search supports CDR3 either including or excluding the conserved start and end residues (ASSAADTQY / CASSAADTQYF both work).
Advanced Query
Similar to the Homepage search, the advanced Receptor search box supports Has sequence, Chain and CDR3 options (see Homepage query for details). Additionally, the receptor type may be selected from a drop-down (e.g., TCR αβ), data may be filtered to include only paired chains, and receptors with specific names in the literature may be found by name.
The Sequence search may be limited to ‘Exact matches’, ‘Substring’ or searching for a homologous match ranging from 90% identity to a 60% identity. The sequence this applies to can be specified in the Region drop down, allowing for either full sequence or CDR1/2/3 matching (CDR3 will also apply to Junction).
The V Gene and J Gene may be searched for, and can be specified on the allele or gene level. Gene level searches will include all alleles for that gene, but allele level searches will only return receptors annotated with that exact allele. For some receptors, allele-level information is not known, and searching at the gene level is therefore recommended.
Since receptor gene names are only meaningful in the context of a given species, the autocomplete options will include species names. It is also possible to directly specify the receptor Species. Usually, the receptor species is the same as the host organism, which can be queried under the ‘Host’ tab. However, some transgenic mouse species may express human TCRs/antibodies (e.g., Mus musculus HuMAb (Medarex)). For these receptors, the receptor species will be human, and the assay host will be mouse.
Flexible Data Export
Data can be exported by clicking ‘Export Results’ in the right upper corner of the results view. As for all data tables, IEDB export options can be customized to different tabular formats (.XLSX/.TSV/.CSV/.JSON and single/double/no headers), and Columns to Include can be flexibly selected. When exporting receptor data, IEDB Receptor ID refers to the individual receptors, and Group IRI contains the group identifier, which links back to the Receptor Details Page.
Curated versus Calculated data in export
In the IEDB receptor exports there are two groups of fields for the VDJ Genes and for the CDR 1, 2, 3 and junction sequences; described as either ‘curated’ or ‘calculated’. Below is the difference between the two types:
- Curated - The curated data are as reported by our team of curators. Typically, these values are as the authors specified them in the original publication, unless informed changes were made to support standardization.
- Calculated - The calculated sequences and genes are the output of our standardization and validation pipeline. A combination of different tools is used to ensure sequence information is presented according to IMGT numbering, and VDJ information matches valid IMGT nomenclature for alleles, genes or subgroups for the given species.
Users are recommended to use the calculated data fields in their computational analyses. The curated fields are kept for reference, and can be used to cross-check information on a case-by-case basis.
Exporting data in AIRR format
To support interoperability with tools from the Adaptive Immune Receptor Repertoire (AIRR) Community, a special option has been added under ‘Export Type’, allowing for direct export of data in AIRR format. This export contains all standard AIRR Rearrangement fields, and additional custom fields marked by the prefix ‘iedb_’. These custom fields describe epitope, MHC and assay information. To ensure direct usage with computational tools, the AIRR format exclusively export Calculated data fields.
For a detailed description, please see the preprint.
