1L7I

Crystal Structure of the anti-ErbB2 Fab2C4

Summary for 1L7I

• Entry DOI: 10.2210/pdb1l7i/pdb
• Descriptor: chimera of Fab2C4: "humanized" murine monoclonal antibody, SULFATE ION, ... (4 entities in total)
• Functional Keywords: ig domain, fab fragment, immune system
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 47414.76

Authors

Vajdos, F.F.,Adams, C.W.,Breece, T.N.,Presta, L.G.,de Vos, A.M.,Sidhu, S.S. (deposition date: 2002-03-15, release date: 2002-07-10, Last modification date: 2024-11-20)

Primary citation

Vajdos, F.F.,Adams, C.W.,Breece, T.N.,Presta, L.G.,de Vos, A.M.,Sidhu, S.S.
Comprehensive functional maps of the antigen-binding site of an anti-ErbB2 antibody obtained with shotgun scanning mutagenesis.
J.Mol.Biol., 320:415-428, 2002

PubMed Abstract: Shotgun scanning combinatorial mutagenesis was used to study the antigen-binding site of Fab2C4, a humanized monoclonal antibody fragment that binds to the extracellular domain of the human oncogene product ErbB2. Essentially all the residues in the Fab2C4 complementarity determining regions (CDRs) were alanine-scanned using phage-displayed libraries that preferentially allowed side-chains to vary as the wild-type or alanine. A separate homolog-scan was performed using libraries that allowed side-chains to vary only as the wild-type or a similar amino acid residue. Following binding selections to isolate functional clones, DNA sequencing was used to determine the wild-type/mutant ratios at each varied position, and these ratios were used to assess the contributions of each side-chain to antigen binding. The alanine-scan revealed that most of the side-chains that contribute to antigen binding are located in the heavy chain, and the Fab2C4 three-dimensional structure revealed that these residues fall into two groups. The first group consists of solvent-exposed residues which likely make energetically favorable contacts with the antigen and thus comprise the functional-binding epitope. The second group consists of buried residues with side-chains that pack against other CDR residues and apparently act as scaffolding to maintain the functional epitope in a binding-competent conformation. The homolog-scan involved subtle mutations, and as a result, only a subset of the side-chains that were intolerant to alanine substitutions were also intolerant to homologous substitutions. In particular, the 610 A2 functional epitope surface revealed by alanine-scanning shrunk to only 369 A2 when mapped with homologous substitutions, suggesting that this smaller subset of side-chains may be involved in more precise contacts with the antigen. The results validate shotgun scanning as a rapid and accurate method for determining the functional contributions of individual side-chains involved in protein-protein interactions.

PubMed: 12079396
DOI: 10.1016/S0022-2836(02)00264-4

Experimental method

X-RAY DIFFRACTION (1.8 Å)