Preliminary refinement and structural analysis of the Fab fragment from human immunoglobulin New at 2.0 Å resolution

The three-dimensional structure of the Fab fragment from human myeloma IgG New has been refined using 'model building' and 'real space' procedures. By these techniques, the correlation between the amino acid sequences and the 2.0 A resolution multiple isomorphous replacement Fourier map has been optimized. The average shift of all atoms during real space refinement was 0.62 A. A list of the refined atomic coordinates for the 440 amino acid residues in the structure is given. Ramachandran plots prepared using the refined coordinates show a distribution of φ, ψ angular values which corresponds to the predominant β-pleated sheet conformation present in the structure. The structures of the homology subunits V(H), V(L), C(H)1, and C(L) were superimposed by pairs and quantitatively compared. The closest similarities were observed between V(H) and V(L) and between C(H)1 and C(L). Amino acid sequence alignments obtained from this structural superposition are given. The closest sequence homology in Fab New is observed between C(H)1 (γ heavy chain) and C(L) (λ light chain). In addition, there is considerable homology between the variable and constant regions. The distances of close contacts between the homology subunits of Fab New have been determined. The closer contacts, those between atoms at a distance ≤1.2 times their van der Waals radii, are analyzed in relation to the constant, variable, and hypervariable nature of the immunoglobulin sequence positions at which they occur. Most of the residues which determine the closer contacts between V(H) and V(L) and between C(H)1 and C(L) are structurally homologous and highly conserved or conservatively replaced in immunoglobulin sequences. The relation between idiotypic determinants, antigen combining site and hypervariable regions, is discussed in terms of the refined model.