IG, TR and IgSF, MHC and MhcSF: What do we learn from the IMGT Colliers de Perles?

Briefings in Functional Genomics and Proteomics

Volumn 6, Issue 4, 2007, Pages 253-264

  Kaas, Quentin ^a   Ehrenmann, François ^b   Lefranc, Marie Paule ^b  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b CNRS   (France)

Author keywords

Domain; Ig like; IMGTCollier de Perles; Immunoglobulin superfamily IgSF; Major histocompatibility complex superfamily MhcSF; Mhc like

Indexed keywords

BETA 2 MICROGLOBULIN; IMMUNOGLOBULIN; IMMUNOGLOBULIN HEAVY CHAIN; IMMUNOGLOBULIN LIGHT CHAIN; MAJOR HISTOCOMPATIBILITY ANTIGEN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2; T LYMPHOCYTE RECEPTOR; T LYMPHOCYTE RECEPTOR ALPHA CHAIN; T LYMPHOCYTE RECEPTOR BETA CHAIN; T LYMPHOCYTE RECEPTOR DELTA CHAIN; T LYMPHOCYTE RECEPTOR GAMMA CHAIN;

AMINO ACID SEQUENCE; ANTIBODY ENGINEERING; ANTIGEN PRESENTING CELL; ANTIGEN STRUCTURE; ARTICLE; BIOINFORMATICS; DNA SEQUENCE; GENE MUTATION; GENETIC POLYMORPHISM; IMMUNOGENETICS; IMMUNOGLOBULIN STRUCTURE; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN STRUCTURE; STANDARDIZATION;

AMINO ACID SEQUENCE; ANIMALS; HUMANS; IMMUNOGENETICS; IMMUNOGLOBULINS; MAJOR HISTOCOMPATIBILITY COMPLEX; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, ANTIGEN, T-CELL;

EID: 46049112076     PISSN: 14739550     EISSN: 14774062     Source Type: Journal    
DOI: 10.1093/bfgp/elm032     Document Type: Article

References (41)

1. Lefranc M-P, Pommié C, Ruiz M, et al. IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev Comp Immunol 2003;27:55-77.
2. Lefranc M-P, Pommié C, Kaas Q, et al. IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Dev Comp Immunol 2005;29:185-203.
3. Duprat E, Kaas Q, Garelle V, et al. IMGT standardization for alleles and mutations of the V-LIKE-DOMAINs and C-LIKE-DOMAINs of the immunoglobulin superfamily. Recent Res Devel Human Genet 2004;2 111-36.
4. Williams AF, Barclay AN. The immunoglobulin superfamily-domains for cell surface recognition. Annu Rev Immunol 1988;6:381-405.
5. Hunkapiller T, Hood L. Diversity of the immunoglobulin gene superfamily. Adv Immunol 1989;44:1-63.
6. Jones EY. The immunoglobulin superfamily. Curr Opin Struct Biol 1993;3:846-52.
7. Bork P, Holm L, Sander C. The immunoglobulin fold. Structural classification, sequence patterns and common core. J Mol Biol 1994;242:309-20.
8. Bertrand G, Duprat E, Lefranc M-P, et al. Characterization of human FCGR3B*02 (HNA-1b, NA2) cDNAs and IMGT standardized description of FCGR3B alleles. Tissue Antigens 2004;64:119-31.
9. Bernard D, Hansen JD, du Pasquier L, et al. Costimulatory receptors in non mammalian vertebrates: Conserved CD28, odd CTLA4 and multiple BTLAs. Dev Comp Immunol 2007; 31:255-71.
10. Garapati VP, Lefranc M-P. IMGT Colliers de Perles and IgSF domain standardization for T cell costimulatory activatory (CD28, ICOS) and inhibitory (CTLA4, PDCD1 and BTLA) receptors. Dev Comp Immunol 2007; 31:1050-72.
11. Kaas Q, Lefranc M-P. T cell receptor/peptide/MHC molecular characterization and standardized pMHC contact sites in IMGT/ 3Dstructure-DB. In Silico Biol 2005; 5:505-28.
12. Lefranc M-P, Duprat E, Kaas Q, et al. IMGT unique numbering for MHC groove G-DOMAIN and MHC superfamily (MhcSF) G-LIKE-DOMAIN. Dev Comp Immunol 2005;29:917-38.
13. Maenaka K, Jones EY. MHC superfamily structure and the immune system. Curr Opin Struct Biol 1999;9:745-53.
14. Duprat E, Lefranc M-P, Gascuel O. A simple method to predict protein binding from aligned sequences - application to MHC superfamily and beta2-microglobulin. Bioinformatics 2006;22:453-9.
15. Frigoul A, Lefranc M-P. MICA: Standardized IMGT allele nomenclature, polymorphisms and diseases. Recent Res Devel Human Genet 2005;3 95-105.
16. Lefranc M-P, Giudicelli V, Kaas Q, et al. IMGT, the international ImMunoGeneTics information system ®. Nucl Acids Res2005;33 D593-7.
17. Giudicelli V, Lefranc M-P. Ontology for immunogenetics: IMGT-ONTOLOGY. Bioinformatics 1999;15:1047-54.
18. Duroux P, Kaas Q, Brochet X, et al. IMGT-Kaleidoscope, the formal IMGT-ONTOLOGY paradigm. Biochimie 2007 Sep 11; [Epub ahead of print].
19. Lefranc M-P, Lefranc G. The Immunoglobulin FactsBook. London: Academic Press, 2001:1-458.
20. Lefranc M-P, Lefranc G. The T cell receptor FactsBook. London: Academic Press, 2001:1-398.
21. Giudicelli V, Chaume D, Lefranc M-P. IMGT/GENE-DB: A comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucl Acids Res 2005;33:D256-61.
22. Lefranc M-P. WHO-IUIS Nomenclature Subcommittee for Immunoglobulins and T cell receptors report. Dev Comp Immunol 2007 Nov 6; [Epub ahead of print].
23. Lefranc M-P, Giudicelli V, Ginestoux C, et al. IMGT-ONTOLOGY for immunogenetics and immunoinformatics (http://imgt.cines.fr). In Silico Biol 2004;4:17-29.
24. Lefranc M-P, Clément O, Kaas Q, et al. IMGT-Choreography for immunogenetics and immunoinformatics (http://imgt.cines.fr). In Silico Biol 2005;29:185-203.
25. Lefranc M-P. Unique database numbering system for immunogenetic analysis. Immunol.Today 1997;18:509.
26. Lefranc M-P. The IMGT unique numbering for immunoglobulins, T cell receptors and Ig-like domains. Immunologist 1999;7:132-6.
27. Giudicelli V, Ginestoux C, Folch G, et al. IMGT/LIGM-DB, the IMGT® comprehensive database of immunoglobulin and T cell receptor nucleotide sequences. Nucleic Acids Res 2006;34:D781-4.
28. Kaas Q, Ruiz M, Lefranc M-P. IMGT/3Dstructure-DB and IMGT/ StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data. Nucleic Acids Res 2004;32 D208-10.
29. Giudicelli V, Chaume D, Lefranc M-P. IMGT/V-QUEST, an integrated software for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis. Nucleic Acids Res 2004;32:W435-40.
30. Yousfi Monod M, Giudicelli V, Chaume D, et al. IMGT/ JunctionAnalysis: The first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics 2004;20:i379-85.
31. Ruiz M, Lefranc M-P. IMGT gene identification and Colliers de Perles of human immunoglobulin with known 3D structures. Immunogenetics 2002;53:857-83.
32. Pommié C, Levadoux S, Sabatier R, et al. IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties. J Mol Recognit 2004; 17:17-32.
33. Kaas Q, Lefranc M-P. IMGT Colliers de Perles: Standardized sequence-structure representations of the IgSF and MhcSF superfamily domains. Curr Bioinformatics 2007; 2:21-30.
34. Gardinier MV, Amiguet P, Linington C, et al. Myelin/ Oligodendrocyte glycoprotein is a unique member of the immunoglobulin superfamily. J Neurosci Res 1992;33:177-87.
35. Schrewe H, Thompson J, Bona M, et al. Cloning of the complete gene for carcinoembryonic antigen: Analysis of its promoter indicates a region conveying cell type-specific expression. Mol Cell Biol 1990;10:2738-48.
36. Cybulsky MI, Fries JWU, Williams AJ, et al. Gene structure, chromosomal location, and basis for alternative mRNA splicing of the human VCAM1 gene. Proc Natl Acad Sci USA 1991;88:7859-63.
37. Wilson IA, Bjorkman PJ. Unusual MHC-like molecules: CD1, Fc receptor, the hemochromatosis gene product, and viral homologs. Curr Opin Immunol 1998;10:67-73.
38. Braud VM, Allan DS, McMichael AJ. Functions of nonclassical MHC and non-MHC-encoded class I molecules. Curr Opin Immunol 1999;11 100-8.
39. Magdelaine-Beuzelin C, Kaas Q, Wehbi V, et al. Structure-function relationships of the variable domains of monoclonal antibodies approved for cancer treatment. Crit Rev Oncol/Hematol 2007;64:210-25.
40. Laffly E, Danjou L, Condemine F, et al. Selection of a macaque Fab with human-like framework regions, high affinity, and that neutralizes the protective antigen (PA) of Bacillus anthracis. Antimicrob Agents Chemother 2005; 49:3414-20.
41. Belessi CJ, Davi FB, Stamatopoulos KE, et al. IGHV gene insertions and deletions in chronic lymphocytic leukemia: 'CLL-biased' deletions in a subset of cases with stereotyped receptors. Eur J Immunol 2006;36: 1963-74.