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IMGT/3Dstructure-DB


NAR Molecular Biology Database Collection entry number 502
Ehrenman, F., Kaas, Q., and Lefranc, M.-P.
Université Montpellier 2, CNRS, Montpellier, FRANCE

Database Description

IMGT/3Dstructure-DB (1,2) is the three-dimensional (3D) structure database of IMGT®, the international ImMunoGenetics information system® (3,4) that is acknowledged as the global reference in immunogenetics and immunoinformatics. IMGT/3Dstructure-DB contains 3D structures of immunoglobulins (IG) (5) or antibodies, T cell receptors (TR) (6), major histocompatibility complex (MHC) proteins, antigen receptor/antigen complexes (IG/Ag, TR/peptide/MHC) of vertebrates; 3D structures of related proteins of the immune system (RPI) of vertebrates and invertebrates, belonging to the immunoglobulin superfamily (IgSF) and MHC superfamily (MhcSF). The IMGT/3Dstructure-DB structural data are extracted from the Protein Data Bank (PDB) (7) and annotated according to the IMGT-ONTOLOGY concepts of classification (8,9), using internal tools and IMGT/DomainGapAlign. IMGT/3Dstructure-DB provides IMGT gene and allele identification (CLASSIFICATION), region and domain delimitations (DESCRIPTION), amino acid positions according to the IMGT unique numbering (NUMEROTATION) (10-12) that are used in IMGT/3Dstructure-DB cards, results of contact analysis and renumbered flat files. IMGT/3Dstructure-DB provides the IMGT Colliers de Perles (13) that are 2D graphical representations based on the IMGT unique numbering, the key IMGT-ONTOLOGY concept of numerotation. IMGT Colliers de Perles are currently available for three domain types: V type (that includes the V-DOMAIN of IG and TR, and V-LIKE-DOMAIN of the IgSF other than IG and TR) (10), C type (that includes the C-DOMAIN of IG and TR, and C-LIKE- DOMAIN of the IgSF other than IG and TR) (11) and G type (that includes the G-DOMAIN of MHC, and G-LIKE-DOMAIN of the MhcSF other than MHC) (12). IMGT/DomainGapAlign tool analyses amino acid sequences, per domain. Coupled to the IMGT/Collier-de-Perles tool, it provides an invaluable help for antibody engineering and humanization design based on complementarity determining region (CDR) grafting as it precisely defines the standardized framework regions (FR-IMGT) and CDR-IMGT. Moreover the IMGT unique numbering facilitates the identification of potential immunogenic residues at given positions in chimeric or humanized antibodies, including those of the constant domains. The IMGT standardization has allowed to build a unique frame for the comparison of the IG, TR and MHC structural data and interactions with their ligands. That standardization has been extended to the IgSF and MhcSF proteins that involve V, C and/or G type domains and used, as an example, to develop a binding prediction method for MhcSF G type domain and beta2-microglobulin (14). IMGT/StructuralQuery (1) is a tool which allows search of IMGT/3Dstructure-DB based on specific structural characteristics (e.g., phi/psi angle, accessible surface area (ASA), distance in angstrom between amino acids). IMGT/3Dstructure-DB was developed and implemented by Manuel Ruiz, Quentin Kaas, François Ehrenmann and Marie-Paule Lefranc, and has been available on the Web since November 2001.

Recent Developments

In October 2009, the IMGT/3Dstructure-DB database manages 1,649 coordinate files which correspond to 1,773 receptors (1092 IG, 89 TR, 387 MHC and 205 RPI).

Acknowledgements

IMGT® received funding from the European Union (EU) programmes BIOMED1(BIOCT930038), BIOTECH2 (BIO4CT960037), 5th PCRDT (QLG2-2000-01287) and 6th PCRDT (ImmunoGrid IST-028069), from the Agence Nationale de la Recherche ANR (BIOSYS06-135457), the Région Languedoc-Roussillon (GPTR, GEPETOS) and from the GIS IBiSA Infrastructures en Biologie Santé et Agronomie (2008-37). IMGT® is funded by the Centre National de la Recherche Scientifique (CNRS), the Ministère de l'Enseignement Supérieur et de la Recherche.

References

1. Kaas, Q., Ruiz, M. and Lefranc, M.-P. (2004), IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data. Nucleic Acids Res. 32, D208-D210
2. Ehrenmann, F., Kaas, Q., and Lefranc, M.-P. (2010) IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF. Nucleic Acids Res., doi:10.1093/nar/gkp946
3. Lefranc, M.-P., Giudicelli, V., Ginestoux, C., Jabado-Michaloud, J., Folch, G., Bellahcene, F., Wu, Y., Gemrot, E., Brochet, X., Lane, J., Regnier, L., Ehrenmann, F., Lefranc, G., and Duroux, P. (2009) IMGT®, the international ImMunoGeneTics information system®. Nucleic Acids Res. 37, D1006-D1012
4. Lefranc, M.-P., Clément, O., Kaas, Q., Duprat, E., Chastellan, P., Coelho, I., Combres, K., Ginestoux, C., Giudicelli, V., Chaume, D., and Lefranc, G. (2005) IMGT-Choreography for Immunogenetics and Immunoinformatics. In Silico Biology 5, 45-60
5. Lefranc, M.-P. and Lefranc, G. (2001) The Immunoglobulin FactsBook, Academic Press, ISBN:012441351X
6. Lefranc, M.-P. and Lefranc, G. (2001) The T cell receptor FactsBook, Academic Press, ISBN:0124413528
7. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235-242
8. Giudicelli, V. and Lefranc, M.-P. (1999) Ontology for immunogenetics: the IMGT-ONTOLOGY. Bioinformatics 15, 1047-1054
9. Duroux, P., Kaas, Q., Brochet, X., Lane, J., Ginestoux, C., Lefranc, M.-P., and Giudicelli, V. (2008) IMGT-Kaleidoscope, the Formal IMGT-ONTOLOGY paradigm. Biochimie 90, 570-583
10. Lefranc, M.-P., Pommié, C., Ruiz, M., Giudicelli, V., Foulquier, E., Truong, L., Thouvenin-Contet, V., and Lefranc, G. (2003) IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev. Comp. Immunol. 27, 55-77
11. Lefranc, M.-P., Pommié, C., Kaas, Q., Duprat, E., Bosc, N., Guiraudou, D., Jean, C., Ruiz, M., Da Piedade, I., Rouard, M., Foulquier, E., Thouvenin, V., and Lefranc G. (2005) IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Dev. Comp. Immunol. 29, 185-203
12. Lefranc, M.-P., Duprat, E., Kaas, Q., Tranne, M., Thiriot, A., and Lefranc, G. (2005) IMGT unique numbering for MHC groove G-DOMAIN and MHC superfamily (MhcSF) G-LIKE-DOMAIN. Dev. Comp. Immunol. 29, 917-938
13. Ruiz, M. and Lefranc, M.-P. (2002) IMGT gene identification and Colliers de Perles of human immunoglobulins with known 3D structures. Immunogenetics 53, 857-883
14. Duprat, E., Lefranc, M.-P., and Gascuel, O. (2006) A simple method to predict protein binding from aligned sequences - application to MHC superfamily and beta2-microglobulin. Bioinformatics 22, 453-459

Subcategory: Protein structure

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