Protein Displays of the Human T Cell Receptor Alpha, Beta...

IMGT Locus in Focus

Exp Clin Immunogenet 2000;17:205–215

Protein Displays of the Human T CellReceptor Alpha, Beta, Gamma andDelta Variable and Joining Regions

Géraldine Folch Dominique Scaviner Valérie ContetMarie-Paule Lefranc

Laboratoire d’ImmunoGénétique Moléculaire, Institut de Génétique Humaine, CNRS,Université Montpellier II, Montpellier, France

Received: January 19, 2000

Prof. Marie-Paule Lefranc, IMGT, Laboratoire d’ImmunoGénétiqueMoléculaire, LIGM, UPR CNRS 1142, IGH, 141 rue de la CardonilleF–34396 Montpellier Cedex 5 (France)Tel. +33 4 99 61 99 65, Fax +33 4 99 61 99 01E-Mail [email protected], IMGT: http://imgt.cines.fr:8104

ABCFax + 41 61 306 12 34E-Mail [email protected]

© 2000 S. Karger AG, Basel0254–9670/00/0174–0205$17.50/0

Accessible online at:www.karger.com/journals/eci

Key WordsHuman W IMGT W T cell receptor W Alphavariable and joining regions W Beta variableand joining regions W Gamma variable andjoining regions W Delta variable and joiningregions

Abstract‘Protein Displays of the Human T Cell Recep-tor Alpha, Beta, Gamma and Delta Variableand Joining Regions’, the 13th report of the‘IMGT Locus in Focus’ section, comprises 8figures: (1) ‘Protein display of the human TRAV-REGIONs’; (2) ‘Protein display of the hu-man TRB V-REGIONs’; (3) ‘Protein display ofthe human TRG V-REGIONs’; (4) ‘Protein dis-play of the human TRD V-REGIONs’; (5) ‘Pro-tein display of the human TRA J-REGIONs’;(6) ‘Protein display of the human TRB J-

REGIONs’; (7) ‘Protein display of the humanTRG J-REGIONs’; (8) ‘Protein display of thehuman TRD J-REGIONs’, and 4 tables enti-tled: (1) ‘FR-IMGT and CDR-IMGT length ofthe human TRAV genes’; (2) ‘FR-IMGT andCDR-IMGT length of the human TRBV genes’;(3) ‘FR-IMGT and CDR-IMGT length of thehuman TRGV genes’; (4) ‘FR-IMGT and CDR-IMGT length of the human TRDV genes’.These figures and tables are available at theIMGT Marie-Paule page from IMGT, the inter-national ImMunoGeneTics database (http://

imgt.cines.fr:8104) created by Marie-PauleLefranc, Université Montpellier II, CNRS,Montpellier, France.

Copyright © 2000 S. Karger AG, Basel

206 Exp Clin Immunogenet 2000;17:205–215 Folch/Scaviner/Contet/Lefranc

‘Protein Displays of the Human T cell Re-ceptor Alpha, Beta, Gamma and Delta Vari-able and Joining Regions’ is the 13th report ofthe ‘IMGT Locus in Focus’ section launchedin the April 1998 issue of Experimental andClinical Immunogenetics [1]. We have pre-viously reported the complete repertoire ofthe human germline TRAV [2] and TRAJ [3],TRBV [4], TRBD and TRBJ [5] genes, local-ized at the TRA (14q11.2) locus and at theTRB locus (7q35), respectively, as well asTRBV orphon genes identified on chromo-some 9 (9p21) [4]. This 13th report completesthese data by providing the protein displaysof the corresponding reference coding regions.It comprises 8 figures: (1) ‘Protein display ofthe human TRA V-REGIONs’; (2) ‘Proteindisplay of the human TRB V-REGIONs’;(3) ’Protein display of the human TRG V-REGIONs’; (4) ‘Protein display of the humanTRD V-REGIONs’; (5) ‘Protein display ofthe human TRA J-REGIONs’; (6) ‘Proteindisplay of the human TRB J-REGIONs’;(7) ‘Protein display of the human TRG J-REGIONs’; (8) ‘Protein display of the hu-man TRD J-REGIONs’; and 4 tables entitled:(1) ‘FR-IMGT and CDR-IMGT length ofthe human TRAV genes’; (2) ‘FR-IMGT andCDR-IMGT length of the human TRBVgenes’; (3) ‘FR-IMGT and CDR-IMGTlength of the human TRGV genes’; (4) ‘FR-IMGT and CDR-IMGT length of the humanTRDV genes’. These figures and tables areavailable at the IMGT Marie-Paule pagefrom IMGT, the international ImMunoGe-neTics database (http://imgt.cines.fr:8104)

created by Marie-Paule Lefranc, UniversitéMontpellier II, CNRS, Montpellier, France[6–9]. Nucleotide and amino acid numberingof the V-REGION is according to the IMGTunique numbering system [1, 10, 11]. De-tailed protein displays of the human TRB D-REGIONs [5] and TRD D-REGIONs areavailable in IMGT Repertoire 1 Alignments

of alleles 1 Human TRBD and TRDD Over-views, respectively.

In figures 1–4, the T cell receptor genes aredesignated according to the IMGT gene tables[2–5] and locus representations (see IMGTRepertoire at IMGT Home page, http://imgt.cines.fr:8104, IMGT Repertoire 11. Lo-cus and Genes). Only FUNCTIONAL andORF V-GENEs are shown. In tables 1–4,numbers in bold, on the second line at the topof each column, represent the IMGT uniquenumbering for the FR-IMGT and CDR-IMGT. Numbers in parentheses, on the thirdline, correspond to the range of FR-IMGTand CDR-IMGT lengths (in number of aminoacids) observed for the TRAV, TRBV, TRGVand TRDV genes (tables 1–4, respectively).Numbers in the CDR1-IMGT, CDR2-IMGTand CDR3-IMGT columns show the CDRlengths in number of amino acids. Informa-tion in the FR1-IMGT, FR2-IMGT and FR3-IMGT columns shows the gaps compared tothe IMGT numbering: the number of missingamino acids is indicated following the sign ‘–’with, in parentheses, the position(s) of themissing amino acid(s) compared to the IMGTnumbering. Columns are left blank if there areno gaps. The proteolytic cleavage site betweenthe leader peptide and the V-REGION is pu-tative and the assignment of amino acid 1(IMGT numbering) to one or the other regionis uncertain.

Fig. 1. Protein display of the human TRA V-RE-GIONs. Only the *01 allele of each functional or ORFV-REGION is shown. Letters in red correspond toamino acids which are polymorphic in the otheralleles. TRAV genes are listed, for each subgroup,according to their position from 5) to 3) in the locus.The 8 amino acids in 5) of TRAV23/DV6 and the 6amino acids in 5) of TRAV29/DV5, as predicted by theprogram SIGSEQ2 and as described by Wülfung andPlückthun [12], are not shown.

Human TRAV, TRBV, TRGV andTRDV Protein Displays

Exp Clin Immunogenet 2000;17:205–215 207

1


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Fig. 5. Protein display of the human TRA J-REGIONs. Only the *01 allele of each functionalor ORF J-REGION is shown. Letters in red correspond to amino acids which are polymorphicin the other alleles and to the conserved motif FGXG. Human TRAJ segments are listed from5) to 3) in the locus.



Fig. 6. Protein display of the hu-man TRB J-REGIONs. Only the*01 allele of each functional orORF J-REGION is shown. The let-ter F (Phe) of TRBJ2–7 corre-sponds to an amino acid which ispolymorphic in another allele. Theconserved motif FGXG is in red.Human TRBJ segments are listedfrom 5) to 3) in the locus.

Fig. 7. Protein display of the hu-man TRG J-REGIONs. Only the*01 allele of each functional orORF J-REGION is shown. Theconserved motif FGXG is in red.

Fig. 8. Protein display of the hu-man TRD J-REGIONs. Only the*01 allele of each functional orORF J-REGION is shown. Theconserved motif FGXG is in red.



Acknowledgments

We thank Nathalie Pallarès and Chantal Ginestouxfor their contribution to the figures, and VéroniqueGiudicelli and Gérard Lefranc for helpful discussion.IMGT is funded by the European Union’s BIOTECH(BIO4CT96–0037) and 5th PCRD programmes, theCNRS (Centre National de la Recherche Scientifique)and the MENRT (Ministère de l’Education Nationale,

de la Recherche et de la Technologie). Subventionshave been received from ARC (Association pour laRecherche sur le Cancer), ARP (Association de laRecherche sur la Polyarthrite), FRM (Fondation pourla Recherche Médicale), Ligue Nationale contre leCancer and the Région Languedoc-Roussillon.

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