IMGT/3Dstructure-DB
NAR Molecular Biology Database Collection entry number 502
Kaas, Q., Ehrenman, F., Lefranc, M.-P.
Université Montpellier 2, CNRS, Montpellier, France.
Contact Marie-Paule.Lefranc@igh.cnrs.fr
Database Description
IMGT/3Dstructure-DB (1) is the IMGT® three-dimensional structure database for immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and related proteins of the immune system (RPI). IMGT/3Dstructure-DB is part of IMGT® (http://imgt.cines.fr/), the international ImMunoGeneTics information system® (2,3), the high-quality integrated knowledge resource specialized in IG (4), TR (5), MHC of human and other vertebrate species, and RPI that belong to the immunoglobulin superfamily (IgSF) and to the MHC superfamily (MhcSF). IMGT/3Dstructure-DB data comprise IG, TR, MHC and RPI with known 3D structures. Coordinate files are extracted from the Protein Data Bank PDB (6), and IMGT annotations are added according to the IMGT Scientific chart rules based on the IMGT-ONTOLOGY axioms and concepts (7,8). IMGT/3Dstructure-DB provides IMGT gene and allele identification (according to the CLASSIFICATION axiom), domain delimitations (according to the DESCRIPTION axiom), amino acid positions (according to the IMGT unique numbering (9-11) based on the NUMEROTATION axiom). Domains that are analysed in IMGT/3Dstructure-DB include V-DOMAIN (variable) and C-DOMAIN (constant) found in IG and TR, V-LIKE and C-LIKE-DOMAINs found in proteins other than IG and TR, G-DOMAIN (groove) found in MHC and G-LIKE-DOMAINs found in proteins other than MHC (9-11). Moreover, IMGT/3Dstructure-DB provides renumbered coordinate flat files, 2D graphical representations (on one and two layers IMGT Collier de Perles (12)), and results of contact analysis. 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). The IMGT unique numbering and gene standardization provide a great help in large scale sequence-structure studies and more generally in protein engineering. IMGT/3Dstructure-DB was implemented by Manuel Ruiz and Quentin Kaas, and has been available on the Web since November 2001.
Recent Developments
In April 2008, the IMGT/3Dstructure-DB database manages 1,423 coordinate files which correspond to 1,510 proteins (941 IG, 80 TR, 315 MHC and 174 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)and from the Région Languedoc-Roussillon. IMGT® is funded by the Centre National de la Recherche Scientifique (CNRS), the Ministère de l'Education Nationale and the Ministère 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. Lefranc, M.-P., Giudicelli, V., Kaas, Q., Duprat, E., Jabado-Michaloud, J., Scaviner, D., Ginestoux, C., Clément, O., Chaume, D., and Lefranc, G. (2005) IMGT, the international ImMunoGeneTics information system®. Nucleic Acids Res., 2005, 33, D593-D597
3. 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, 2005, 5, 45-60.
4. Lefranc, M.-P., and Lefranc, G. (2001) The Immunoglobulin FactsBook (http://imgt.cines.fr/textes/IMGTindex/factsbook.html), Academic Press, 458 pages, ISBN:012441351X
5. Lefranc, M.-P., and Lefranc, G. (2001) The T cell receptor FactsBook (http://imgt.cines.fr/textes/IMGTindex/factsbook.html), Academic Press, 398 pages, ISBN: 0124413528
6. 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
7. Giudicelli, V., and Lefranc, M.-P. (1999) Ontology for immunogenetics: the IMGT-ONTOLOGY. Bioinformatics, 15, 1047-1054
8. 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.
9. 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.
10. 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
11. 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.
12. Ruiz, M., and Lefranc, M.-P. (2002) IMGT gene identification and Colliers de Perles of human immunoglobulins with known 3D structures. Immunogenetics, 2002, 53, 857-883.
2. Lefranc, M.-P., Giudicelli, V., Kaas, Q., Duprat, E., Jabado-Michaloud, J., Scaviner, D., Ginestoux, C., Clément, O., Chaume, D., and Lefranc, G. (2005) IMGT, the international ImMunoGeneTics information system®. Nucleic Acids Res., 2005, 33, D593-D597
3. 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, 2005, 5, 45-60.
4. Lefranc, M.-P., and Lefranc, G. (2001) The Immunoglobulin FactsBook (http://imgt.cines.fr/textes/IMGTindex/factsbook.html), Academic Press, 458 pages, ISBN:012441351X
5. Lefranc, M.-P., and Lefranc, G. (2001) The T cell receptor FactsBook (http://imgt.cines.fr/textes/IMGTindex/factsbook.html), Academic Press, 398 pages, ISBN: 0124413528
6. 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
7. Giudicelli, V., and Lefranc, M.-P. (1999) Ontology for immunogenetics: the IMGT-ONTOLOGY. Bioinformatics, 15, 1047-1054
8. 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.
9. 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.
10. 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
11. 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.
12. Ruiz, M., and Lefranc, M.-P. (2002) IMGT gene identification and Colliers de Perles of human immunoglobulins with known 3D structures. Immunogenetics, 2002, 53, 857-883.
Category: Structure Databases
Subcategory: Protein structure
Go to the abstract in the NAR 2004 Database Issue.
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