Information Technology Reference
In-Depth Information
1.5 IMGT-ONTOLOGY Concepts and IMGT
®
Components
for 2D and 3D Structures
1.5.1 IMGT
®
Structural Database
The IMGT
®
structural approach refers to the study of the 2D and 3D structures of the
IG, TR, MHC, and RPI, and to the antigen or ligand binding characteristics in rela-
tion to the protein functions, polymorphisms, and evolution. The structural approach
relies on the CLASSIFICATION concept (IMGT gene and allele names),
DESCRIPTION concept (receptor and chain description, domain delimitations), and
NUMEROTATION concept (amino acid positions according to the IMGT unique
numbering) (Lefranc et al. 2003; Lefranc et al. 2005b; Lefranc et al. 2005c). Struc-
tural and functional domains of the IG and TR chains comprise the variable domain
or V-DOMAIN (nine-strand β-sandwich) that corresponds to the V-J-REGION or
V-D-J-REGION and is encoded by two or three genes (Lefranc and Lefranc 2001a;
Lefranc and Lefranc 2001b; Lefranc et al. 2003), the constant domain or
C-DOMAIN (seven-strand β-sandwich) (Lefranc et al. 2005b), and, for the MHC
chains, the groove domain or G-DOMAIN (four β-strand and one α-helix) (Lefranc
et al. 2005c). The IMGT unique numbering has been extended to the V-LIKE-
DOMAINs (Lefranc et al. 2003) and C-LIKE-DOMAINs (Lefranc et al. 2005b) of
IgSF proteins other than IG and TR, and to the G-LIKE-DOMAINs (Lefranc et al.
2005c) of MhcSF proteins other than MHC.
Structural data are compiled and annotated in IMGT/3Dstructure-DB.
IMGT/3Dstructure-DB is the IMGT
®
3D structure database for IG, TR, MHC, and
RPI, created by LIGM, on the Web since November 2001 (Kaas, Ruiz, and Lefranc
2004). In March 2007, IMGT/3Dstructure-DB contained 1221 atomic coordinate
files. IMGT/3Dstructure-DB comprises IG, TR, MHC, and RPI with known 3D
structures. Coordinate files extracted from the Protein Data Bank PDB (Berman,
Westbrook, Feng, Gilliland, Bhat, Weissig, Shindyalov, and Bourne 2000) (http://
www.rcsb.org/pdb/)
are renumbered according to the standardized IMGT unique
numbering (Lefranc et al. 2003; Lefranc et al. 2005b; Lefranc et al. 2005c). The
IMGT/3Dstructure-DB cards provide IMGT annotations (assignment of IMGT genes
and alleles, IMGT chain and domain labels, IMGT Colliers de Perles for V, C, and G
type domains (Ruiz and Lefranc 2002; Kaas and Lefranc 2005; Kaas and Lefranc
2007), downloadable renumbered IMGT/3Dstructure-DB flat files, visualization
tools, and external links. The IMGT/3Dstructure-DB residue cards provide detailed
information on the inter- and intra-domain contacts of each residue position. An
IMGT/3Dstructure-DB card provides receptor and chain description, IMGT gene and
allele names, domain delimitations, and amino acid positions according to the IMGT
unique numbering. Standardized IMGT pMHC contact sites have been defined for
peptide/MHC complexes (Kaas and Lefranc 2005).
