IMGT/3Dstructure-DB

Other names: IMGT/3Dstructure-DB and IMGT/2Dstructure-DB, ImMunoGeneTics/3Dstructure-DB and IMGT/2Dstructure-DB, International ImMunoGeneTics information system/3Dstructure-DB and IMGT/2Dstructure-DB, IMGT 3Dstructure-DB, imgt_3dstructure

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.

Webpage:
http://www.imgt.org/

Licence:
Name: Copyrights
URL: http://www.imgt.org/ligmdb/

Publications:

Tags:

structure protein structure amino acid sequences antibodies genetics immunoglobulins proteins immunoinformatics immunology small molecule model organisms immunogenetics

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