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IMGT unique numbering for C-DOMAIN and C-LIKE-DOMAIN

Citing IMGT unique numbering for C-DOMAIN and C-LIKE-DOMAIN:
Lefranc, M.-P. et al., Dev. Comp. Immunol., 29, 185-203 (2005) PMID: 15572068 pdf with permission from Elsevier

New 'IMGT Protein display for C domain' header: pdf doc

IMGT unique numbering for C-DOMAIN

The C-DOMAIN corresponds to the complete C-REGION, to most of the C-REGION or to only part of the C-REGION, depending on the immunoglobulin (IG) or T cell receptor (TR) chain type.

The IMGT numbering for C-DOMAIN (IG and TR) [1] is derived as the IMGT unique numbering for V-DOMAIN [2], from the princeps IMGT unique numbering for V-REGION, up to position 104. Positions 105 to 128 were defined by comparing C-DOMAIN and V-DOMAIN [2]. Amino acid positions can therefore be easily compared between the C-DOMAIN and the V-DOMAIN[1].

Amino acid positions shown on the upper line in the Protein displays correspond to equivalent positions in the V-DOMAIN. The correspondence was established by sequence alignment comparison and structural data analysis (Ruiz M., Martinez-Jean C and Lefranc M.-P. IMGT on-line, 27/02/2001). Amino acid positions on the lower line are characteristic of the C-DOMAIN.

We can distinguish:

IMGT unique numbering for C-LIKE-DOMAIN

The C-LIKE-DOMAIN corresponds to a domain of similar structure as C-DOMAIN, found in chains other than IG or TR.

The IMGT unique numbering for C-LIKE-DOMAIN (proteins other than IG or TR) follows exactly the same rules are those of the C-DOMAIN.

The IMGT unique numbering for the C-LIKE-DOMAIN and V-LIKE-DOMAIN allows, for the first time, to compare any C-LIKE-DOMAIN and V-LIKE-DOMAIN of any protein of the immunoglobulin superfamily (IgSF).

Range of strand, turn and loop lengths in C-DOMAIN and C-LIKE-DOMAIN

The range of the strand, turn and loop lengths from 51 selected examples of C-DOMAIN and C-LIKE-DOMAIN [1] is indicated between parentheses. The total length of the domain is between 85 and 110 amino acids for 46 of the 51 examples [1]. Start and end positions of the A, B, C, CD, D, E, F and G strands, of the AB, DE and EF turns, and of the BC and FG loops are according to [1].

A
strand
AB
turn
B
strand
BC
loop
C
strand
CD
strand
D
strand
DE
turn
E
strand
EF
turn
F
strand
FG
loop
G
strand
Total
length
1.8-1.1,
1-15
15.1-15.3 16-26 27-38 39-45 45.1-45.7 77-84 84.1-84.7,
85.7-85.1
85-96 96.1-96.2 97-104 105-117,
111.1-111.6,
112.1-112.6
118-128
(6-23) (0-2) (7-11) (4-10) (7) (0-7) (4-8) (0-14) (8-12) (0-2) (4-8) (7-25) (4-10) (67-129)

Detailed rules

Gaps and additional position rules for FG-LOOP

These rules follow those of V-DOMAIN CDR3-IMGT.

The basic length of a FG-LOOP is 13 amino acids (positions 105 to 117).

If the FG-LOOP length is less than 13 amino acids, gaps are created from the top of the loop, in the following order 111, 112, 110, 113, 109, 114, etc.

FG-LOOP
lengths
Gaps for FG-LOOP lengths < 13 amino acids
13 105 106 107 108 109 110 111 112 113 114 115 116 117
12 105 106 107 108 109 110 - 112 113 114 115 116 117
11 105 106 107 108 109 110 - - 113 114 115 116 117
10 105 106 107 108 109 - - - 113 114 115 116 117
9 105 106 107 108 109 - - - - 114 115 116 117
8 105 106 107 108 - - - - - 114 115 116 117
7 105 106 107 108 - - - - - - 115 116 117
6 105 106 107 - - - - - - - 115 116 117
5 105 106 107 - - - - - - - - 116 117
---

If the FG-LOOP length is more than 13 amino acids, additional positions are created between positions 111 and 112 at the top of the FG loop in the following order 112.1,111.1, 112.2, 111.2, 112.3, 111.3, etc.

FG-LOOP
lengths
Additional positions between 111 and 112 for FG-LOOP lengths > 13 amino acids
---
21 111 111.1 111.2 111.3 111.4 112.4 112.3 112.2 112.1 112
20 111 111.1 111.2 111.3 - 112.4 112.3 112.2 112.1 112
19 111 111.1 111.2 111.3 - - 112.3 112.2 112.1 112
18 111 111.1 111.2 - - - 112.3 112.2 112.1 112
17 111 111.1 111.2 - - - - 112.2 112.1 112
16 111 111.1 - - - - - 112.2 112.1 112
15 111 111.1 - - - - - - 112.1 112
14 111 - - - - - - - 112.1 112
References:
[1] Lefranc, M.-P. et al., Dev. Comp. Immunol., 29, 185-203 (2005) PMID: 15572068 LIGM:293 pdf with permission from Elsevier
[2] Lefranc, M.-P. et al., Dev. Comp. Immunol., 27, 55-77 (2002) PMID: 12477501 LIGM:268
Acknowledgements:
We thank Elsevier and Developmental and Comparative Immunology, for allowing IMGT to make available the DCI pdf file on the IMGT site.
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