Particularities in protein designations: Human immunoglobulins: New and Newm

Click here to see Part 1 - Discrepancies between protein names in publications and databases.

Part 2 - Protein displays showing the discrepancies between sequences.

Click here to see Protein New.

Protein Newm
V-DOMAINs
       IGL V-J-REGION
       IGH V-D-J-REGION
C-DOMAINs
       IGL C-REGION
       IGH CH1

V-DOMAINs

_____________________________________________________________________________________________________________________________________________________________________
 IGL V-J-REGION                         FR1-IMGT           CDR1-IMGT      FR2-IMGT      CDR2-IMGT                 FR3-IMGT                   CDR3-IMGT    FR4-IMGT
                                           (1-26)             (27-38)        (39-55)       (56-65)                  (66-104)                   (105-117)    (118-127)
_______________________________ __________________________ ____________ _________________ __________ _______________________________________ _____________ __________
                                1       10        20         30         40        50         60         70        80        90       100        110        120
                                .........|.........|...... ...|........ .|.........|..... ....|..... ....|.........|.........|.........|.... .....|....... ..|.......
M94116     ,IGLV1-40*01 (1)     QSVLTQPPS.VSGAPGQRVTISCTGS SSNIGAGYD... VHWYQQLPGTAPKLLIY GNS....... NRPSGVP.DRFSGSK..SGTSASLAITGLQAEDEADYYC QSYDSSLSG....
                                                                                                                                                         
[1]                             pSVLTQPPS.VSGAPGQRVTISCTGS SSNIGAGNH... VKWYQQLPGTAPKLLIF HNN....... -------.ARFSVSK..SGSSATLAITGLQAEDEADYYC QSYDR....SLRV FGGGTKLTVL
[2]                             ZSVLTQPPS.VSGAPGQRVTISCTGS SSNIGAGNH... VKWYQQLPGTAPKLLIF HNN....... -------.ARFSVSK..SGSSATLAITGLQAEDEADYYC QSYDR....SLRV FGGGTKLTVL
[3]                             ZSVLTQPPS.VSGAPGQRVTISCTGS SSNIGAGHN... VKWYQQLPGTAPKLLIF HNN....... -------.ARFSVSK..SGTSATLAITGLQAEDEADYYC QSYDR....SLRV FGGGTKLTVL
GenPept    ,L1HUNM g69828       QSVLTQPPS.VSGAPGQRVTISCTGS SSNIGAGNH... VKWYQQLPGTAPKLLIF HNN....... -------.ARFSVSK..SGSSATLAITGLQAEDEADYYC QSYDR....SLRV FGGGTKLTVL
GenPept    ,AAB24270 g260395    ZSVLTQPPS.VSGAPGQRVTISCTGS SSNIGAGHN... VKWYQQLPGTAPKLLIF HNN....... -------.ARFSVSK..SGTSATLAITGLQAEDEADYYC QSYDR....SLRV FGGGTKLTVL
Kabat      ,007549              pSVLTQPPS.VSGAPGQRVTISCTGS SSNIGAGNH... VKWYQQLPGTAPKLLIF HNN....... -------.ARFSVSK..SGSSATLAITGLQAEDEADYYC QSYDR....SLRV FGGGTKLTVL
PIR        ,L1HUNM A01968       QSVLTQPPS.VSGAPGQRVTISCTGS SSNIGAGNH... VKWYQQLPGTAPKLLIF HNN....... -------.ARFSVSK..SGSSATLAITGLQAEDEADYYC QSYDR....SLRV FGGGTKLTVL
SWISS-PROT ,P01703              QSVLTQPPS.VSGAPGQRVTISCTGS SSNIGAGNH... VKWYQQLPGTAPKLLIF HNN....... -------.ARFSVSK..SGSSATLAITGLQAEDEADYYC QSYDR....SLRV FGGGTKLTVL
PDB        ,7fab                ASVLTQPPS.VSGAPGQRVTISCTGS SSNIGAGHN... VKWYQQLPGTAPKLLIF HNN....... -------.ARFSVSK..SGTSATLAITGLQAEDEADYYC QSYDR....SLRV FGGGTKLTVL


Legend:
  • Sequences are shown according to the chronological order of the publications.
  • p: pyrrolidone carboxylic acid.
    In green, indetermination in the protein sequence or extrapolation from other sequences. In blue, discrepancies between amino acid sequences in databases and publications. Cysteines involved in the disulphide bridge are shown in red.
  • Amino acid numbering of the rearranged CDR3-IMGT [105-117] and of the FR4-IMGT [118-127] is according to the IMGT unique numbering for V-DOMAINs. Gaps have been created at positions 110-113 by comparison to a "13 amino acid long" rearranged CDR3-IMGT sequence.
    Amino acids 105-109 and 114-116 belong to the V-REGION, and amino acids 117-127 to the J-REGION

IMGT note:
(1)Probable germline IGLV gene involved in the Newm rearrangement identified by IMGT curators (M. Ruiz, O. Posukh and M.-P. Lefranc Marie-Paule.Lefranc@igh.cnrs.fr).
The IGL V-J Newm rearrangement is the following: IGLV1-40*01-IGLJ2*01 (or IGLJ3*01 or IGLJ3*02).



______________________________________________________________________________________________________________________________________________________________________
 IGH V-D-J-REGION                      FR1-IMGT           CDR1-IMGT      FR2-IMGT      CDR2-IMGT                 FR3-IMGT                    CDR3-IMGT    FR4-IMGT
                                          (1-26)             (27-38)        (39-55)       (56-65)                  (66-104)                    (105-117)    (118-128)
_______________________________ __________________________ ____________ _________________ __________ _______________________________________ _____________ ___________
                                1       10        20         30         40        50         60         70        80        90       100         110       120
                                .........|.........|...... ...|........ .|.........|..... ....|..... ....|.........|.........|.........|.... .....|....... ..|........
L10088     ,IGHV4-59 (1)        QVQLQESGP.GLVKPSETLSLTCTVS GGSISSYY.... WSWIRQPPGKGLEWIGY IYYSGST... NYNPSLK.SRVTISVDTSKNQFSLKLSSVTAADTAVYYC AR...........
                                                                                                                                                       
[5]                             ZVQLPESGP.ELVSPGZTLSLTCTGS TVSTFAVY.... IVWVRQPPGRGLEWIGY VFYHGTS... DTDTPLR.SRVTMLVNTSKNQFSLRLSSVTAADTAVYYC ARBLIA..GCIBV WGQGSLVTVSS
[4]                             pVQLEQSGP.GLVRPSQTLSLTCTVS GSTFSNDY.... YTWVRQPPGRGLEWIGY VFYHGTS... DDTTPLR.SRVTMLVDTSKNQFSLRLSSVTAADTAVYYC ARNLIA..GCIDV WGQGSLVTVSS
[2]                             ZVQLEQSGP.GLVRPSQTLSLTCTVS GSTFSNDY.... YTWVRQPPGRGLEWIGY VFYHGTS... DTDTPLR.SRVTMLVNTSKNQFSLRLSSVTAADTAVYYC ARNLIA..GCIDV WGQGSLVTVSS
[3]                             ZVQLEQSGP.GLVRPSQTLSLTCTVS GTSFDDYY.... WTWVRQPPGRGLEWIGY VFYTGTT... LLDPSLR.GRVTMLVNTSKNQFSLRLSSVTAADTAVYYC ARNLIA..GCIDV WGQGSLVTVSS
GenPept    ,G1HUNM g69974       QVQLEQSGP.GLVRPSQTLSLTCTVS GSTFSNDY.... YTWVRQPPGRGLEWIGY VFYHGTS... DDTTPLR.SRVTMLVDTSKNQFSLRLSSVTAADTAVYYC ARNLIA..GCIDV WGQGSLVTVSS
Kabat      ,000838              pVQLZZSGP.GLVRPSQTLSLTCTVS GSTFSNDY.... YTWVRQPPGRGLEWIGY VFYHGTS... DDTTPLR.SRVTMLVDTSKNQFSLRLSSVTAADTAVYYC ARNLIA..GCIDV WGQGSLVTVSS
PDB        ,7fab                AVQLEQSGP.GLVRPSQTLSLTCTVS GTSFDDYY.... WTWVRQPPGRGLEWIGY VFYTGTT... LLDPSLR.GRVTMLVNTSKNQFSLRLSSVTAADTAVYYC ARNLIA..GGIDV WGQGSLVTVSS


Legend:
  • Sequences are shown according to the chronological order of the publications.
  • p: pyrrolidone carboxylic acid.
    In green, indetermination in the protein sequence or extrapolation from other sequences. In blue, discrepancies between amino acid sequences in databases and publications. Cysteines involved in the disulphide bridge are shown in red.
  • Amino acid numbering of the rearranged CDR3-IMGT [105-117] and of the FR4-IMGT [118-128] is according to the IMGT unique numbering for V-DOMAINs. Gaps have been created at positions 111-112 by comparison to a "13 amino acid long" rearranged CDR3-IMGT sequence.
    Amino acids 105-106 belong to the V-REGION, 107-110 and 113-115 to the N-AND-D-REGION, and amino acids 116-117 to the J-REGION
  • .

IMGT note:
(1)Probable germline IGHV gene involved in the Newm rearrangement identified by IMGT curators (M. Ruiz, O. Posukh and M.-P. Lefranc Marie-Paule.Lefranc@igh.cnrs.fr).
The IGH V-D-J Newm rearrangement is the following: IGHV4-59*04-IGHJ6*01 (or IGHJ6*02).




C-DOMAINs

_____________________________________________________________________________________________________________________________________________________________________________________________

IGL C-REGION

_____________________________________________________________________________________________________________________________________________________________________________________________
                               A                 B         BC         C               D                     E              F               G
                         -------------->    ---------->             ----->        ----------->       -------------->  ------------->   ---------->
                          1       10   15  16  20 23      30    36 39 41 45      77     84             85  89     96 97    104   110 114   120       130       140       150
                    654321|........|....|123|...|...... ...|.....|  |.....|1234567|......|12345677654321|..........|12|............|...|.....|.........|.........|.........|
J00254 ,IGLC3*01 (1)  QPKAAPSVTLFPPSSEELQ...ANKATLVCLIS DFYP..GAVT  VAWKADSSPVK.AGVETTTPSKQSNN.......KYAASSYLSLTPEQW..KSHKSYSCQVTHE....GSTVEKTVAPTECS

[2]and [5]            QPKAAPSVTLFPPSSEELQ...ANKATLVCLIS DFYP..GAVT  VAWKADSSPVK.AGVETTTPSKQSNN.......KYAASSYLSLTPEQW..KSHKSYSCQVTHE....GSTVEKTVAPTECS
[3]                   QPKAAPSVTLFPPSSEELQ...ANKATLVCLIS DFYP..GAVT  VAWKADGSPVK.AGVETTTPSKQSNN.......KYAASSYLSLTPEQW..KSHKSYSCQVTHE....GSTVEKTVAPTECS
Kabat   ,013784       QPKAAPSVTLFPPSSZZLQ...ANKATLVCLIS DFYP..GAVT  VAWKADSSPVK.AGVETTTPSKQSNN.......KYAASSYLSLTPEQW..KSHKSYSCZVTHE....GSTVEKTVAPTECS
PIR     ,L2HU A90375  QPKAAPSVTLFPPSSEELQ...ANKATLVCLIS DFYP..GAVT  VAWKADSSPVK.AGVETTTPSKQSNN.......KYAASSYLSLTPEQW..KSHRSYSCQVTHE....GSTVEKTVAPTECS


Legend:
  • Sequences are shown according to the chronological order of the publications.
  • In blue, discrepancies between amino acids sequences in databases and publications. Cysteines involved in the disulphide bridge are shown in red.

IMGT note:
(1)Translation of the genomic IGLC3*01 C-REGION. IGLC3*01 and IGLC3*03 only differ by silent mutations.
S45 and K100 correspond to the serological markers Ke- Oz+, respectively.



_____________________________________________________________________________________________________________________________________________________________________________________________

IGH CH1(1)

_____________________________________________________________________________________________________________________________________________________________________________________________
                               A                 B         BC         C               D                     E              F               G
                         -------------->    ---------->             ----->        ----------->       -------------->  ------------->   ---------->
                          1       10   15  16  20 23      30    36 39 41 45      77     84             85  89     96 97    104   110 114   120       130       140       150
                    654321|........|....|123|...|...... ...|.....|  |.....|1234567|......|12345677654321|..........|12|............|...|.....|.........|.........|.........|
J00228  ,IGHG1(2)   (A)STKGPSVFPLAPSSKSTS...GGTAALGCLVK DYFP..EPVT  VSWNSGALTS....GVHTFPAVLQSS......GLYSLSSVVTVPSSSL...GTQTYICNVNHKP..SNTKVDKKV

[5]           (3)   (A)STKGPSVFPLAPSSKSTS...GGTAALGCLVK DYFP..EPVT  VSWNSGALTS....GVHTFPAVLQSS......GLYSLSSVVTVPSSSL...GTQTYICNVNHKP..SNTKVDKRVEPKSC
[2]and [3]    (3)   (A)STKGPSVFPLAPSSKSTS...GGTAALGCLVK DYFP..EPVT  VSWNSGALTS....GVHTFPAVLQSS......GLYSLSSVVTVPSSSL...GTQTYICNVNHKP..SNTKVDKKVEPKSC


Legend:
  • Sequences are shown according to the chronological order of the publications.
  • In blue, discrepancies between amino acids sequences in databases and publications. Cysteines involved in the disulphide bridge are shown in red.

IMGT notes:
(1) For the Newm heavy gamma-1 chain, only the CH1 C-DOMAIN is displayed.
(2) Translation of the genomic IGHG1*01 CH1 exon.
(3) The last 5 amino acids (EPKSC) belong to the beginning of the hinge region.



References:
[1] Chen, B.L. and Poljak, R.J., Biochemistry, 13, 1295-1302 (1974). PMID:4814727
[2] Saul, F.A., Amzel, L.M. and Poljak, R.J., J. Biol. Chem., 253, 585-597 (1978). PMID:618887
[3] Saul, F.A. and Poljak, R.J., Proteins, 14, 363-371 (1992). MEDLINE:93066153
[4] Poljak, R.J. et al., Biochemistry, 16, 3412-3420 (1977). PMID:407927
[5] Poljak, R.J. et al., Proc. Natl. Acad. Sci. USA, 71, 3440-3444 (1974). PMID:4215080


Created: 03/04/2001
Author: Lisa Truong

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