title: The structural repertoire of the human V kappa domain.
abstract: In humans, the gene for the V kappa domain is produced by the recombination of one of 40 functional V kappa segments and one of five functional J kappa segments. We have analysed the sequences of these germline segments and of 736 rearranged V kappa genes to determine the repertoire of main chain conformations, or canonical structures, they encode. Over 96% of the sequences correspond to one of four canonical structures for the first antigen binding loop (L1) and one canonical structure for the second antigen binding loop (L2). Junctional diversity produces some variation in the length of the third antigen binding loop (L3) and in the identity of residues at the V kappa-J kappa join. However, this is limited and 70% of the rearranged sequences correspond to one of three known canonical structures for the L3 region. Furthermore, we show that the canonical structures selected during the primary response are conserved during affinity maturation: the key residues that determine the conformations of the antigen binding loops are unmutated or undergo conservative mutation. The implications of these results for immune recognition are discussed.
authors.affiliation: MRC Centre for Protein Engineering, University of Cambridge, UK.
authors.forename: I M
authors.initials: IM
authors.lastname: Tomlinson
authors.forename: J P
authors.initials: JP
authors.lastname: Cox
authors.forename: E
authors.initials: E
authors.lastname: Gherardi
authors.forename: A M
authors.initials: AM
authors.lastname: Lesk
authors.forename: C
authors.initials: C
authors.lastname: Chothia
mesh_terms: D000595:Amino Acid Sequence; D001666:Binding Sites, Antibody / Q000235:genetics / Q000276:immunology; D015321:Gene Rearrangement; D005803:Genes, Immunoglobulin; D005854:Germ Cells; D006801:Humans; D007133:Immunoglobulin Joining Region / Q000737:chemistry / Q000235:genetics / Q000276:immunology; D007135:Immunoglobulin Variable Region / Q000737:chemistry* / Q000235:genetics / Q000276:immunology; D007145:Immunoglobulin kappa-Chains / Q000737:chemistry* / Q000235:genetics / Q000276:immunology; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid; D013329:Structure-Activity Relationship
chemical_list: D007133:Immunoglobulin Joining Region; D007135:Immunoglobulin Variable Region; D007145:Immunoglobulin kappa-Chains