3L5X

Crystal structure of the complex between IL-13 and H2L6 FAB

Summary for 3L5X

• Entry DOI: 10.2210/pdb3l5x/pdb
• Related: 3L5W 3L5Y
• Descriptor: H2L6 LIGHT CHAIN, H2L6 HEAVY CHAIN, Interleukin-13, ... (6 entities in total)
• Functional Keywords: immunoglobulin fold, alpha-helical bundle, cytokine, disulfide bond, glycoprotein, polymorphism, secreted, monoclonal antibody, immune system
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 60375.36

Authors

Teplyakov, A.,Obmolova, G.,Malia, T.,Gilliland, G.L. (deposition date: 2009-12-22, release date: 2010-04-14, Last modification date: 2023-09-06)

Primary citation

Fransson, J.,Teplyakov, A.,Raghunathan, G.,Chi, E.,Cordier, W.,Dinh, T.,Feng, Y.,Giles-Komar, J.,Gilliland, G.,Lollo, B.,Malia, T.J.,Nishioka, W.,Obmolova, G.,Zhao, S.,Zhao, Y.,Swanson, R.V.,Almagro, J.C.
Human framework adaptation of a mouse anti-human IL-13 antibody.
J.Mol.Biol., 398:214-231, 2010

PubMed Abstract: Humanization of a potent neutralizing mouse anti-human IL-13 antibody (m836) using a method called human framework adaptation (HFA) is reported. HFA consists of two steps: human framework selection (HFS) and specificity-determining residue optimization (SDRO). The HFS step involved generation of a library of m836 antigen binding sites combined with diverse human germline framework regions (FRs), which were selected based on structural and sequence similarities between mouse variable domains and a repertoire of human antibody germline genes. SDRO consisted of diversifying specificity-determining residues and selecting variants with improved affinity using phage display. HFS of m836 resulted in a 5-fold loss of affinity, whereas SDRO increased the affinity up to 100-fold compared to the HFS antibody. Crystal structures of Fabs in complex with IL-13 were obtained for m836, the HFS variant chosen for SDRO, and one of the highest-affinity SDRO variants. Analysis of the structures revealed that major conformational changes in FR-H1 and FR-H3 occurred after FR replacement, but none of them had an evident direct impact on residues in contact with IL-13. Instead, subtle changes affected the V(L)/V(H) (variable-light domain/variable-heavy domain) interface and were likely responsible for the 5-fold decreased affinity. After SDRO, increased affinity resulted mainly from rearrangements in hydrogen-bonding pattern at the antibody/antigen interface. Comparison with m836 putative germline genes suggested interesting analogies between natural affinity maturation and the engineering process that led to the potent HFA anti-human IL-13 antibody.

PubMed: 20226193
DOI: 10.1016/j.jmb.2010.03.004

Experimental method

X-RAY DIFFRACTION (1.9 Å)