IMGT/3Dstructure-DB
NAR Molecular Biology Database Collection entry number 502
Kaas, Q., Ruiz, M., Lefranc, M.-P.
Université Montpellier II, CNRS, Montpellier, FRANCE
Contact kaas@ligm.igh.cnrs.fr
Database Description
IMGT/3Dstructure-DB is the IMGT three dimensional structure database for immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), and related proteins of the immune system (RPI) of human and other vertebrate species (1). IMGT/3Dstructure-DB is part of IMGT (http://imgt.cines.fr/), the international ImMunoGeneTics information system® (2), the high-quality integrated knowledge resource specializing in IG (3), TR (4), and RPI of human and other vertebrate species. IMGT/3Dstructure-DB data comprise IG, TR, MHC and RPI with known 3D structures. Coordinate files are extracted from the Protein Data Bank PDB (5), and IMGT annotations are added according to the IMGT Scientific chart rules based on the IMGT-ONTOLOGY concepts (6). IMGT/3Dstructure-DB provides IMGT gene and allele identification (according to the CLASSIFICATION concept), domain delimitations (according to the DESCRIPTION concept), amino acid positions (according to the IMGT unique numbering (7) based on the NUMEROTATION concept). 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 (8). Moreover, IMGT/3Dstructure-DB provides renumbered coordinate flat files, 2D graphical representations (standard and two layer Collier de Perles (9)), and results of contact analysis. The IMGT unique numbering and gene standardization will 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. The IMGT/3Dstructure-DB database manages 634 coordinate files which correspond to 417 different proteins (260 IG, 18 TR and 144 MHC).
Recent Developments
IMGT/StructuralQuery (10) is a new 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).
Acknowledgements
IMGT is funded by the European Union's 5th PCRDT programme QLG2-2000-01287, the Centre National de la Recherche Scientifique (CNRS), the Ministère de l'Education Nationale and the Ministère de la Recherche.
References
1. Kaas Q. and Lefranc M.-P., IMGT/3Dstructure-DB for immunoglobulin, T cell receptor and MHC structural data, European Conference in Computational Biology ECCB 2002, P72, 2002
2. Lefranc, M.-P., IMGT, the international ImMunoGeneTics database®, Nucleic Acids Res., 2003, 31, 307-310, PMID:12520009
3. Lefranc M.-P. and Lefranc G., The Immunoglobulin FactsBook, Academic Press, Harcourt, 458 pages, 2001, ISBN:012441351X
4. Lefranc M.-P. and Lefranc G., The T cell receptor FactsBook, Academic Press, Harcourt, 398 pages, 2001, ISBN:0124413528
5. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N. and Bourne P.E., The Protein Data Bank, Nucleic Acids Res., 2000, 28, 235-242, PMID:10592235
6. Giudicelli V. and Lefranc M.-P., Ontology for immunogenetics: the IMGT-ONTOLOGY, Bioinformatics, 1999, 15, 1047-1054, PMID: 10745995
7. Lefranc M.-P., Pommié C., Ruiz M., Giudicelli V., Foulquier E., Truong L., Thouvenin-Contet V. and Lefranc G., IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev. Comp. Immunol., 2003, 27, 55-77, PMID:12477501
8. Duprat E. and Lefranc M.-P., IMGT standardization and analysis of V-LIKE6, C-LIKE- and G-LIKE-DOMAINs, European Conference in Computational Biology ECCB 2003
9. Ruiz M. and Lefranc M.-P., IMGT gene identification and Colliers de Perles of human immunoglobulins with known 3D structures. Immunogenetics, 2002, 53, 857-883, PMID:11862387
10. Kaas Q. and Lefranc M.-P., IMGT/StructuralQuery : a tool for structural data analysis of immunoglobulin and T cell receptor variable domains, European Conference in Computational Biology ECCB 2003
2. Lefranc, M.-P., IMGT, the international ImMunoGeneTics database®, Nucleic Acids Res., 2003, 31, 307-310, PMID:12520009
3. Lefranc M.-P. and Lefranc G., The Immunoglobulin FactsBook, Academic Press, Harcourt, 458 pages, 2001, ISBN:012441351X
4. Lefranc M.-P. and Lefranc G., The T cell receptor FactsBook, Academic Press, Harcourt, 398 pages, 2001, ISBN:0124413528
5. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N. and Bourne P.E., The Protein Data Bank, Nucleic Acids Res., 2000, 28, 235-242, PMID:10592235
6. Giudicelli V. and Lefranc M.-P., Ontology for immunogenetics: the IMGT-ONTOLOGY, Bioinformatics, 1999, 15, 1047-1054, PMID: 10745995
7. Lefranc M.-P., Pommié C., Ruiz M., Giudicelli V., Foulquier E., Truong L., Thouvenin-Contet V. and Lefranc G., IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev. Comp. Immunol., 2003, 27, 55-77, PMID:12477501
8. Duprat E. and Lefranc M.-P., IMGT standardization and analysis of V-LIKE6, C-LIKE- and G-LIKE-DOMAINs, European Conference in Computational Biology ECCB 2003
9. Ruiz M. and Lefranc M.-P., IMGT gene identification and Colliers de Perles of human immunoglobulins with known 3D structures. Immunogenetics, 2002, 53, 857-883, PMID:11862387
10. Kaas Q. and Lefranc M.-P., IMGT/StructuralQuery : a tool for structural data analysis of immunoglobulin and T cell receptor variable domains, European Conference in Computational Biology ECCB 2003
Category: Structure Databases
Subcategory: Protein structure
Go to the abstract in the NAR 2004 Database Issue.
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