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Guiraudou, Jean, Ruiz, Da Piedade, Rouard, Foulquier, Thouvenin, and Lefranc
2005d). An IMGT unique numbering has also been set up for the MHC G-
DOMAIN and the G-LIKE-DOMAIN of the MhcSF proteins other than MHC
(Lefranc, Duprat, Kaas, Tranne, Thiriot, and Lefranc 2005b).
The IMGT standardization has allowed the construction of a unique frame for the
comparison of the TR, peptide, and MHC interactions in the different resources
provided by the IMGT
®
information system. IMGT/3Dstructure-DB (Kaas et al.
2004), the IMGT structural database, is used with the IMGT sequence databases,
IMGT/LIGM-DB (Lefranc 2003a; Giudicelli, Ginestoux, Folch, Jabado-Michaloud,
Chaume, and Lefranc 2006) and IMGT/MHC-DB (Robinson, Waller, Parham,
de Groot, Bontrop, Kennedy, Stoehr, and Marsh 2003); the IMGT gene database,
IMGT/GENE-DB (Giudicelli, Chaume, and Lefranc 2005); the IMGT tools for se-
quence analysis, IMGT/V-QUEST (Giudicelli, Chaume, and Lefranc 2004),
IMGT/JunctionAnalysis (Yousfi Monod, Giudicelli, Chaume, and Lefranc 2004);
and the IMGT tool for 3D structure analysis, IMGT/StructuralQuery (Kaas et al.
2004), to explore the TR and MHC conserved structural features. In this paper, we
describe the IMGT standardized rules that have been set up for the molecular charac-
terization of the TR/pMHC complexes. Coordinate files are from IMGT/3Dstructure-
DB (Kaas et al. 2004), http://imgt.cines.fr, with original crystallographic data from
the Protein Data Bank, PDB (Berman, Westbrook, Feng, Gilliland, Bhat, Weissig,
Shindyalov, and Bourne 2000). Eleven IMGT pMHC contact sites were defined (C1
to C11) which can be used to compare pMHC interactions (Kaas and Lefranc 2005).
2.2 T Cell Receptor/Peptide/MHC 3D Structures
and IMGT Standardization
IMGT/3Dstructure-DB (Table 1) contains 18 TR/pMHC structures: 14 (12 TR/
pMHC-I and 2 TR/pMHC-II) with complete extracellular regions of the
α
-
β
TR (TR-
ALPHA_BETA) and 4 structures with an Fv variable fragment (FV-ALPHA_BETA).
The
α
-
β
TR chains, TR-ALPHA and TR-BETA, are described with standardized
IMGT labels in Fig. 1.
The references for the 18 TR/pMHC 3D structures are: 1ao7 (Garboczi, Ghosh,
Utz, Fan, Biddison, and Wiley 1996), 1qrn, 1qse, 1qsf (Ding, Baker, Garboczi,
Biddison and Wiley 1999), 1bd2 (Ding, Smith, Garboczi, Utz, Biddison, and Wiley
1998), 1oga (Stewart-Jones, McMichael, Bell, Stuart, and Jones 2003), 1mi5
(Kjer-Nielsen et al. 2003), 1lp9 (Buslepp, Wang, Biddison, Appella, and Collins
2003), 1g6r (Degano, Garcia, Apostolopoulos, Rudolph, Teyton, and Wilson 2000),
1jtr, 1mwa (Luz, Huang, Garcia, Rudolph, Apostolopoulos, Teyton, and Wilson
2002), 2ckb (Garcia, Degano, Pease, Huang, Peterson, Teyton, and Wilson 1998),
1fo0 (Reiser, Darnault, Guimezanes, Gregoire, Mosser, Schmitt-Verhulst, Fontecilla-
Camps, Malissen, Housset, and Mazza 2000), 1nam (Reiser, Darnault, Gregoire,
Mosser, Mazza, Kearney, van der Merwe, Fontecilla-Camps, Housset, and Malissen
2003), 1kj2 (Reiser, Gregoire, Darnault, Mosser, Guimezanes, Schmitt-Verhulst,
Fontecilla-Camps, Mazza, Malissen, and Housset 2002), 1fyt (Hennecke, Carfi, and
