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Rules for the gap and additional positions in C-DOMAIN and C-LIKE-DOMAIN

A strand (positions 1.8 to 1.1, 1-15)

Table 1. Length of the A and B strands and gaps at the AB turn. Gaps are based on 3D structures in this table. If 3D structures are not known, gaps are equally distributed on strands A and B with, for an odd number, one more gap on strand A.

Number of gaps at the AB turn Examples A strand
1.8-1.1, 1-15
B strand
16-26
Species Gene Domain Number of additional positions at the N-terminus Gap positions A strand length (16-24) Gap positions B strand length (8-11)
0 Homo sapiens IGHG1 CH1, CH3 4   19   11
Homo sapiens IGHG1 CH2 6   21   11
2 Mus musculus CD1D C-LIKE [D3] 1 15 15 16 10
3 Homo sapiens HLA-B C-LIKE [D3] 1 14 15 14 16 10
4 Homo sapiens TRAC C-ALPHA 5 12 13 14 15 16 16 10
7 Homo sapiens TRDC C-DELTA 6 10 12 13 14 15 16 16 17 18 8

AB turn additional positions (positions 15.1-15.3)

C-DOMAINs and C-LIKE-DOMAINs may have additional amino acids (potentially 3) at the AB turn. The number of additional positions at the AB turn defines the AB length (Table 2).

Table 2. Length of the AB turn

Number of additional positions Examples AB additional positions AB length
(0-3)
Species Gene Domain
0 Homo sapiens IGHG1 CH1, CH3   0
1 Homo sapiens TRBC2 C-BETA2 15.1 1
2 Homo sapiens IGHG1 CH2 15.1 15.2 2
3 Homo sapiens CD4 C-LIKE [D2] 15.1 15.2 15.3 3

B strand (positions 16-26)

BC loop (positions 27-38)

The maximum length of the BC loop is 10 amino acids. If the number of amino acids is odd, there is one more amino acid position on the left (Table 3). There are no positions 32 and 33 in C-DOMAINs and C-LIKE-DOMAINs.

Table 3. Length of the BC loop

Number of gaps Examples BC gap positions (1) BC length
(6-10)
Species Gene Domain
0 Homo sapiens IGHG1 CH2   10
Homo sapiens IGHE CH3   10
1 Mus musculus IGHE CH3 34 9
2 Homo sapiens IGHG1 CH1, CH3 31 34 8
3 Homo sapiens TRAC C-ALPHA 31 34 35 7
4 Mus musculus IGHD CH1 30 31 34 35 6

C strand (positions 39-45)

The maximal length of the C strand is 7 amino acids.

CD transversal strand (positions 45.1-45.7)

The CD transversal strand is characteristic of the C-DOMAIN and C-LIKE-DOMAIN. In contrast, there are no C' and C" strands (that is no positions 46 to 76). The maximum length of the CD strand in the usual Collier de Perles is 7 amino acids, however CD strands of 9 amino acids are found in Teleostei IGIC (Table 4). Amino acid positions 45.1 to 45.7 are added from left to right in sequence alignments.

Table 4. Length of the CD transversal strand

Number of amino acid positions Examples CD additional positions CD length
(0-7)
Species Gene Domain
0 Homo sapiens TRAC C-ALPHA   0
1 Homo sapiens CD4 C-LIKE [D4] 45.1 1
Homo sapiens TRDC C-DELTA
2 Homo sapiens FCGR1A C-LIKE [D1] 45.1 to 45.2 2
3 Homo sapiens FCGR1A C-LIKE [D2] 45.1 to 45.3 3
Homo sapiens IGHG1 CH1
4 Homo sapiens IGHG1 CH2, CH3 45.1 to 45.4 4
5 Homo sapiens TRBC2 C-BETA2 45.1 to 45.5 5
Homo sapiens TRGC1 C-GAMMA1
Homo sapiens HLA-B C-LIKE [D3]
6 Homo sapiens IGHA1 CH3 45.1 to 45.6 6
7 Sus scrofa IGHE CH3 45.1 to 45.7 7

D strand (positions 77-84)

Table 5. Gaps at the DE turn. Gaps are based on 3D structures in this table. If 3D structures are not known, gaps at the DE turn are equally distributed on strands D an E with, for an odd number, one more gap on strand D.

Number of gaps at the DE turn Examples D strand
77-84
E strand
85-96
Species Gene Domain Gap positions D strand length (5-8) Gap positions E strand length (10-12)
0 Homo sapiens IGHG1 CH1, CH2, CH3   8   12
4 Homo sapiens FCGR1A C-LIKE [D2] 83 84 6 85 86 10
5 Homo sapiens FCGR1A C-LIKE [D1] 82 83 84 5 85 86 10

DE turn additional positions (positions 84.1-84.7, 85.7-85.1)

Most of the C-DOMAINs and C-LIKE-DOMAINs have additional amino acids (potentially 14) at the DE turn which extend the D and E antiparallel beta strands (Table 6). The number of additional positions at the DE turn defines the DE turn length.

Table 6. Length of the DE turn

Number of additional positions Examples DE additional positions (2) DE length
(6-14)
Species Gene Domain
6 Mus musculus IGHE CH1 84.1 to 84.3, 85.1 to 85.3 6
4 Homo sapiens TRDC C-DELTA 84.1 to 84.4, 85.1 to 85.4 8
8 Homo sapiens TRGC1 C-GAMMA1 84.1 to 84.4, 85.1 to 85.4 8
8 Homo sapiens IGHG1 CH1, CH2, CH3 84.1 to 84.4, 85.1 to 85.4 8
9 Mus musculus TRBC2 C-BETA2 84.1 to 84.5, 85.1 to 85.4 9
10 Canis lupus familiaris IGHA CH3 84.1 to 84.5, 85.1 to 85.5 10
11 Homo sapiens IGHA1 CH3 84.1 to 84.6, 85.1 to 85.5 11
12 Homo sapiens IGHM CH2 84.1 to 84.6, 85.1 to 85.6 12
13 Homo sapiens TRBC2 C-BETA2 84.1 to 84.7, 85.1 to 85.6 13
14 Homo sapiens TRAC C-ALPHA 84.1 to 84.7, 85.1 to 85.7 14

E strand (positions 85-96)

Table 7. Gaps at the EF turn. Gaps are based on 3D structures in this table. If 3D structures are not known, gaps are based on sequence alignments.

Number of gaps at the EF turn Examples E strand
85-96
F strand
97-104
Species Gene Domain Gap positions E strand length
(8-12)
Gap positions F strand length
(4-8)
0 Homo sapiens IGHG1 CH2, CH3   12   8
1 Homo sapiens FCGR2A C-LIKE [D1] 85 86 96 9   8
Homo sapiens IGHG1 CH1 96 11   8
2 Bos taurus IGHG1 CH1 96 11 97 7
Homo sapiens TRGC1 C-GAMMA1 96 11 97 7
3 Homo sapiens HLA-B C-LIKE [D3] 95 96 10 97 7
Rattus norvegicus IGHG2B CH1 91 92 (3) 10 97 7
4 Homo sapiens TRDC C-DELTA 95 96 10 97 98 6
Oryctolagus cuniculus IGHG CH1 95 96 10 97 98 6
8 Homo sapiens TRAC C-ALPHA 93 94 95 96 8 97 98 99 100 4

EF turn additional positions (96.1-96.2)

C-DOMAINs and C-LIKE-DOMAINs may have additional amino acids (potentially 2) at the EF turn. The number of additional positions defines the EF length.

Table 8. Length of the EF turn

Number of additional positions Examples EF additional positions EF length
(0-2)
Species Gene Domain
0 Homo sapiens IGHG1 CH1, CH2, CH3   0
1 Homo sapiens TRBC2 C-BETA2 96.1 1
2 Homo sapiens IGHM CH1 96.1 96.2 2

F strand (positions 97-104)

FG loop (positions 105-117)

Except for the TRBC sequences (Table 10), the maximal length of the FG loop is 13 amino acids (Table 9). For an odd number of gaps, there is one more gap on the left (starting with position 111). TRBC sequences have an insertion of 12 positions between 111 and 112. The length of the FG loop in TRBC is 25 amino acids (Table 10).

Table 9. Length of the FG loop (except TRBC)

Number of gaps Examples FG gap positions FG length
(7-13)
Species Gene Domain
0 Homo sapiens IGHE CH1   13
1 Mus musculus TRAC C-ALPHA 111 12
Homo sapiens IGHG1 CH3
2 Homo sapiens IGHG1 CH1 CH2 111 112 11
3 Homo sapiens FCGR2A C-LIKE [D2] 110 111 112 10
4 Ovis aries IGHA CH2 110 111 112 113 9
6 Homo sapiens FCGR2A C-LIKE [D1] 109 110 111 112 113 114 7

Table 10. Length of the FG loop of TRBC

Number of additional positions Examples FG additional positions (4) FG length
(25)
Species Gene Domain
12 Homo sapiens TRBC2 C-BETA2 111.1 to 111.6, 112.1 to 112.6 25
12 Mus musculus TRBC2 C-BETA2 111.1 to 111.6, 112.1 to 112.6 25

G strand (positions 118-128)

The maximal length of the G strand is 11 amino acids. Positions are filled in, starting from position 118 and depending on the G strand length.

IMGT notes:
(1) Gap positions start with 34, then 31, 35, 30.
(2) The numbering of the additional positions starts positions next to 84 and 85, respectively, towards the top of the DE turn (gap positions 85, 86 shown in italics, for Homo sapiens FCGR2A). If the number of additional amino acids is odd, there is one more position on the left.
(3) Gaps were assigned by sequence alignment with the CH1 of IGHG2A and IGHG2C CH1.
(4) The numbering of the additional positions starts positions next to 111 and 112, respectively, towards the top of the FG loop.