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2.2.1 TR V-DOMAINs
The V-DOMAINs have an immunoglobulin fold, that is an antiparallel
β
sheet
sandwich structure with nine strands (Lefranc et al. 2003b; Lesk and Chothia 1982),
the A, B, E, and D strands being on one sheet, and the G, F, C, C', and C” strands on
the other sheet. These strands are indicated in the IMGT Colliers de Perles (Fig. 2)
and in the IMGT Protein displays (Fig. 3).
IMGT Colliers de Perles are IMGT 2D graphical representations based on the
IMGT unique numbering. The IMGT Colliers de Perles of TR V-DOMAINs are
based on the IMGT unique numbering for V-DOMAIN and V-LIKE-DOMAIN
(Lefranc et al. 2003b) and can be displayed on one layer or on two layers. IMGT
Colliers de Perles of the V-ALPHA and V-BETA domains from 1ao7 (Garboczi
et al. 1996) are shown as examples in Fig. 2. The IMGT Protein display (Fig. 3)
shows the amino acid sequences of the different V-ALPHA and V-BETA domains
found in TR/pMHC (Table 1).
The V-ALPHA and V-BETA domains share main conserved characteristics of
the V-DOMAIN which are the disulfide bridge between cysteine 23 (1st-CYS) and
cysteine 104 (2nd-CYS), and the other hydrophobic core residues tryptophan 41
(CONSERVED-TRP) and leucine (or hydrophobic) 89 (Lefranc et al. 2003b) (Figs.
2 and 3). The A strand comprises positions 1 to 15, B strand positions 16 to 26, C
strand positions 39 to 46, C' strand positions 47 to 55, C” strand positions 66 to 74,
D strand positions 75 to 84, E strand positions 85 to 96, F strand positions 97 to 104,
and G strand positions 118 to 128 (Lefranc et al. 2003b). Compared to the general V-
DOMAIN 3D structure, the V-ALPHA domains have shorter C” and D strands at the
C” D turn.
The three hypervariable loops or complementarity determining regions (CDR) of
each V-DOMAIN are involved in the pMHC recognition. The CDR1-IMGT com-
prises positions 27 to 38, the CDR2-IMGT positions 56 to 65, and the CDR3-IMGT
positions 105 to 117 (Lefranc et al. 2003b). The CDR3-IMGT corresponds to the
junction resulting from the V-J and V-D-J rearrangement, and is more variable in
sequence and length than the CDR1-IMGT and CDR2-IMGT that are encoded by the
V-REGION only (Lefranc and Lefranc 2001). Lengths of the CDR-IMGT are shown
separated by dots between brackets (Lefranc et al. 2003b). Lengths of the CDR-
IMGT from available TR/pMHC 3D structures are reported in Table 1, together with
the names of the V, D, and J genes (Lefranc and Lefranc 2001).
For example, 1ao7 [6.6.11] V-ALPHA means that in the V-ALPHA domain of
1ao7, CDR1-IMGT has a length of 6 amino acids, CDR2-IMGT a length of amino
acids, and CDR3-IMGT a length of 11 amino acids. The V-ALPHA CDR3-IMGT
results from the TRAV12-2-TRAJ24 rearrangement (Table 1, Fig. 3). In the same
way, 1ao7 [5.6.14] V-BETA means that in the V-BETA domain of 1ao7, CDR1-
IMGT, CDR2-IMGT, and CDR3-IMGT have a length of 5, 6, and 14 amino acids,
respectively (Lefranc et al. 2003b). The V-BETA CDR3-IMGT results from the
TRBV6-5-TRBD2-TRBJ2-7 rearrangement (Table 1, Fig. 3).
