About STCRDab

• STCRDab is a database of TCR structures that updates on a weekly basis. It automatically collects and curates information from the PDB on a weekly basis.
• Where present, STCRDab also annotates the MHC molecule that is bound by a TCR. However, STCRDab does not annotate entries that only contain an MHC molecule.
• STCRDab has been built by the Oxford Protein Informatics Group (OPIG).

What is...

• a TCR? A T-cell receptor (TCR) is a protein of the immune system; they are found on the surfaces of T-cells, and typically bind peptides presented on a Major Histocompatibility Complex (MHC) molecule. Most TCRs are made of two protein chains: either TCRβ and TCRα (to form αβ TCRs) or TCRδ and TCRγ (to form γδ TCRs)
• a β/α/δ/γ chain? These chains form a pair to make a TCR. Typically β/α chains and δ/γ chains pair up. Any other chain combinations are considered unpaired.
• a CDR? The complementarity-determining regions (CDRs) are hypervariable loops on the TCR molecule; they tend to have the greatest level of sequence and structural diversity between different TCRs. The CDRs are often involved in antigen binding.
• a canonical form? The canonical forms refer to a number of common conformations that are adopted by CDRA1, CDRA2, CDRA3, CDRB1, CDRB2, and CDRB3 loops. More information can be found in the CDR search page. Given the availability of structural data, the canonical forms for CDRA3 and CDRB3 are for reference purposes.
• an antigen? Any foreign molecule bound by the TCR and presented by the MHC.
• an MHC? An MHC molecule is a protein that is expressed on various cell types. They typically present peptides. There are four types that are represented in STCRDab: MHC Class I (MH1), MHC Class II (MH2), Cluster of differentiation 1 (CD1), and Major histocompatibility complex class I-related protein (MR1).
• the IMGT numbering scheme, germline? The IMGT numbering scheme and germline are nomenclature systems that allow direct comparison between different T-cell receptors and MHC molecules. Further details can be found here. The germline refers to the allele that codes for the T-cell receptor or MHC molecule; again, we use the IMGT nomenclature, and more details can be found here.
• TRangle? The TRangles represent the orientation between the variable domains of the T-cell receptor. It is based on the ABangle methodology by Dunbar et al. (2014). This feature is currently only enabled for αβTCRs. There are six parameters:

  BA the torsion angle between B1 and A1 BC1 the bend angle between B1 and C BC2 the bend angle between B2 and C AC1 the bend angle between A1 and C AC2 the bend angle between A2 and C dc the length of C

• TRangle/ABangle distance? The TRangle/ABangle distance represents the Euclidean norm between the TRangle/ABangle parameters of two TCR structures or a TCR/antibody structure. Structures are considered to be similar in orientation if the distance is less than 10.
• Docking angle? The docking angle of the TCR represents the angle at which the TCR engages with the MHC. It is based on the calculation by Rudolph et al. (2006).

Available data files

In STCRDab, there are two types of files that are readily downloadable:

1. Summary file: this is a tab-separated text file which can be opened in a text editor or a spreadsheet application (e.g. Microsoft Excel; indicate that the file is separated by a tab!).
• The first row is the header (each field explained below).
• Every subsequent row contains information about each set of TCRs (paired or unpaired) along with annotations:
  pdb Bchain Achain Dchain Gchain TCRtype ...
2pye E D NA NA abTCR ...
2. PDB file: structures are available either as an annotated PDB file (re-numbered using ANARCI) or as a non-annotated PDB file, raw from the PDB.
• IMGT-numbered PDB files have some information at the header of the PDB to indicate TCR pairings; for example, in 2pye:
  REMARK 5 PAIRED_ABTCR BCHAIN=E ACHAIN=D AGCHAIN=C AGTYPE=PEPTIDE
• IMGT numbering is applied to variable domains of the TCR and the G-domains of an MHC molecule, or the β2 microglobulin chain.
• Non-annotated PDB files are in the same format as those from the PDB.

Summary file headers

The following fields can be found in each summary file:

pdb	The PDB code of the entry
Bchain	The name of the β chain, if present; else "NA"
Achain	The name of the α chain, if present; else "NA"
Dchain	The name of the γ chain, if present; else "NA"
Gchain	The name of the δ chain, if present; else "NA"
TCRtype	Detected TCR type; either "abTCR" (for αβTCR) or "gdTCR" (for γδTCR) or "NA" for single-domain cases.
model	Model number; defaults to 0 for structures solved by X-ray crystallography.
antigen_chain	The name of the antigen (i.e. non-TCR/non-MHC) chain, if present; else "NA"
antigen_type	Type of antigen. Either "peptide", "protein", "hatpen" or "carbohydrate".
antigen_name	Name of the antigen.
antigen_het_name	The HETATM name of the antigen.
mhc_type	Type of MHC unit. Either MH1, MH2, CD1, MR1 if present; else "NA".
mhc_chain1	This is either MH1, CD1 or MR1 (for MHC class I, CD1 or MR1 proteins) or GA (for MHC class II), if present; else "NA"
mhc_chain2	This is either B2M (for MHC class I, CD1 or MR1 proteins) or GB (for MHC class II), if present; else "NA"
docking_angle	Docking angle between the TCR and MHC
beta_subgroup	The IMGT subgroup for the β chain
alpha_subgroup	The IMGT subgroup for the α chain
delta_subgroup	The IMGT subgroup for the δ chain
gamma_subgroup	The IMGT subgroup for the γ chain
short_header	A short description of the structure from the PDB entry.
date	Deposition date of the structure.
compound	Name of the structure from the PDB.
beta_organism	The organism of the structure's β chain according to the PDB.
alpha_organism	The organism of the structure's α chain according to the PDB.
delta_organism	The organism of the structure's δ chain according to the PDB.
gamma_organism	The organism of the structure's γ chain according to the PDB.
antigen_organism	The organism of the structure's antigen chain(s) according to the PDB.
mhc_chain1_organism	The organism of the structure's first MHC chain (see mhc_chain1) according to the PDB.
mhc_chain2_organism	The organism of the structure's second MHC chain (see mhc_chain2) according to the PDB.
authors	Name(s) of author(s) that deposited the structure.
resolution	Resolution of the structure in Å.
method	Method used to solve the structure.
r_free	R-free value of the structure.
r_factor	R-factor value of the structure.
affinity	Affinity of the TCR, if present; else "NA"
affinity_method	Method used to measure the affinity.
affinity_temperature	Temperature of the conditions during affinity measurement. "NA" if unavailable.
affinity_pmid	Pubmed ID for publication with affinity measurement.
engineered	Indicates whether or not the structure is engineered.

Download method

1. Summary and PDB files are made for each entry separately.
2. Zip files are made for your search results, which contains all the PDB file(s) [ both raw and in the IMGT numbering scheme ] and summary information.

• J. Nowak, T. Baker, G. Georges, S. Kelm, S. Klostermann, J. Shi, S. Sridharan and C.M. Deane. Length-independent structural similarities enrich the antibody CDR canonical class model, mAbs, 2016, 8(4):751-760 [Paper Link]
• M.S. Klausen, M.V. Anderson, M.C. Jespersen, M. Nielsen and P. Marcatili. LYRA, a webserver for lymphocyte receptor structural modeling. Nucleic Acids Res, 2015, 43(W1):W349-355 [Paper Link]
• J. Dunbar, B. Knapp, A. Fuchs, J. Shi and C.M. Deane. Examining variable domain orientations in antigen receptors gives insight into TCR-like antibody design, PLOS Comput Biol, 2014, 10(9):e1003852 [Paper Link]
• M. G. Rudolph, R. L. Stanfield, and I.A. Wilson. How TCRs bind MHCs, peptides, and coreceptors., Annu Rev Immunol, 2006, 24:419-466 [Paper Link]
• B. al-Lazikani, A.M. Lesk, C. Chothia. Canonical structures for the hypervariable regions of T cell alpha beta receptors., J Mol Biol, 2000, 295(4):979-95 [Paper Link]

• Feel free to contact us at for any issues or misannotations or general enquiries about STCRDab.