IMGT Standardization for Molecular Characterization of the T Cell Receptor/Peptide/MHC Complexes - Immunoinformatics - page 19

Chapter 2
IMGT Standardization for Molecular Characterization
of the T Cell Receptor/Peptide/MHC Complexes
Quentin Kaas, 1 Elodie Duprat, 1 Guillaume Tourneur, 1 and Marie-Paule Lefranc 1,2
1 IMGT ® , the International ImMunoGeneTics Information System ® , Université Montpellier
II, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de
Génétique Humaine IGH, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
2 Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France,
[e-mail]
Abstract. One of the key elements in the adaptive immune response is the presentation of
peptides by the major histocompatibility complex (MHC) to the T cell receptors (TR) at the
surface of T cells. The characterization of the TR/peptide/MHC trimolecular complexes
(TR/pMHC) is crucial to the fields of immunology, vaccination, and immunotherapy. In order
to facilitate data comparison and cross-referencing between experiments from different laboratories
whatever the receptor, the chain type, the domain, or the species, IMGT ® , the international
ImMunoGeneTics information system (http://imgt.cines.fr), has developed IMGT-
ONTOLOGY, the first ontology in immunogenetics and immunoinformatics. In IMGT/
3Dstructure-DB, the IMGT three-dimensional structure database, the molecular characteriza-
tion of the TR/pMHC is made according to the IMGT Scientific chart rules that are
based on the IMGT-ONTOLOGY concepts. IMGT/3Dstructure-DB provides the standardized
IMGT gene and allele names (CLASSIFICATION), the standardized IMGT labels
(DESCRIPTION), and the IMGT unique numbering (NUMEROTATION). As the IMGT
structural unit is the domain, amino acids at conserved positions always have the same number
in the IMGT ® databases, tools, and Web resources. For the TR α and β chains, the amino acids
in contact with the peptide/MHC (pMHC) are defined according to the IMGT unique number-
ing for V-DOMAIN. The MHC chain cleft that binds the peptide is formed by two groove
domains (G-DOMAIN), each one comprising four antiparallel β strands and one α helix. The
IMGT unique numbering for G-DOMAIN applies both to the first two domains (G-ALPHA1
and G-ALPHA2) of the MHC class I α chain, and to the first domain (G-ALPHA and
G-BETA) of the MHC class II α chain and β chain, respectively. Based on the IMGT unique
numbering, we defined 11 contact sites for the analysis of the pMHC contacts. The TR/pMHC
contact description, based on the IMGT numbering, can be queried in the IMGT/Stuc-
turalQuery tool, at http://imgt.cines.fr.
2.1 Introduction
T cells are implicated in the specific immune response against a stress of viral, bacte-
rial, fungal, or tumoral origin. They identify antigenic peptides presented by the major
histocompatibility complex (MHC) cell surface glycoproteins. The recognition is