PDBsum entry 3l7e

Immune system

PDB id: 3l7e

Contents

Protein chains

213 a.a. *

216 a.a. *

Ligands

SO4 ×2

GOL

ACT ×2

Waters ×174

* Residue conservation analysis

PDB id:

3l7e

Name:

Immune system

Title:

Crystal structure of anti-il-13 antibody c836

Structure:

C836 light chain. Chain: l, a. Fragment: chimeric molecule of mouse variable domain and human constant domain. Engineered: yes. C836 heavy chain. Chain: h, b. Fragment: fd fragment of the heavy chain, chimeric molecule of mouse variable domain and human constant domain.

Source:

Mus musculus, homo sapiens. Organism_taxid: 10090,9606. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell: human embryonic kidney (hek) 293 cells. Expression_system_cell: human embryonic kidney (hek) 293 cells

Resolution:

2.50Å R-factor: 0.204 R-free: 0.251

Authors:

A.Teplyakov,G.Obmolova,T.Malia,G.L.Gilliland

Key ref:

J.Fransson et al. (2010). Human framework adaptation of a mouse anti-human IL-13 antibody. J Mol Biol, 398, 214-231. PubMed id: 20226193

Date:

28-Dec-09 Release date: 10-Nov-10

Protein chains

No UniProt id for this chain

Struc: 213 a.a.

Protein chains

No UniProt id for this chain

Struc: 216 a.a.

J Mol Biol 398:214-231 (2010)

PubMed id: 20226193

Human framework adaptation of a mouse anti-human IL-13 antibody.

J.Fransson, A.Teplyakov, G.Raghunathan, E.Chi, W.Cordier, T.Dinh, Y.Feng, J.Giles-Komar, G.Gilliland, B.Lollo, T.J.Malia, W.Nishioka, G.Obmolova, S.Zhao, Y.Zhao, R.V.Swanson, J.C.Almagro.

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.