PDBsum entry 2vxv

Immune system

PDB id: 2vxv

Contents

Protein chains

222 a.a. *

214 a.a. *

Ligands

CXS

GOL

Waters ×576

* Residue conservation analysis

PDB id:

2vxv

Name:

Immune system

Title:

Crystal structure of human igg abt-325 fab fragment

Structure:

Human igg abt-325. Chain: h. Engineered: yes. Human igg abt-325. Chain: l. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Expression_system_cell_line: cho. Expression_system_tissue: ovary. Other_details: abt-325 is a recombinant human monoclonal antibody, derived by in vitro selection of human immunoglobulin libraries..

Resolution:

1.49Å R-factor: 0.155 R-free: 0.179

Authors:

M.A.Argiriadi,T.Xiang,C.Wu,T.Ghayur,D.W.Borhani

Key ref:

M.A.Argiriadi et al. (2009). Unusual water-mediated antigenic recognition of the proinflammatory cytokine interleukin-18. J Biol Chem, 284, 24478-24489. PubMed id: 19553661 DOI: 10.1074/jbc.M109.023887

Date:

10-Jul-08 Release date: 23-Jun-09

Protein chain

No UniProt id for this chain

Struc: 222 a.a.

Protein chain

No UniProt id for this chain

Struc: 214 a.a.

DOI no: 10.1074/jbc.M109.023887

J Biol Chem 284:24478-24489 (2009)

PubMed id: 19553661

Unusual water-mediated antigenic recognition of the proinflammatory cytokine interleukin-18.

M.A.Argiriadi, T.Xiang, C.Wu, T.Ghayur, D.W.Borhani.

ABSTRACT

The unique cytokine interleukin-18 (IL-18) acts synergistically with IL-12 to regulate T-helper 1 and 2 lymphocytes and, as such, seems to underlie the pathogenesis of various autoimmune and allergic diseases. Several anti-IL-18 agents are in clinical development, including the recombinant human antibody ABT-325, which is entering trials for autoimmune diseases. Given competing cytokine/receptor and cytokine/receptor decoy interactions, understanding the structural basis for recognition is critical for effective development of anti-cytokine therapies. Here we report three crystal structures: the murine antibody 125-2H Fab fragment bound to human IL-18, at 1.5 A resolution; the 125-2H Fab (2.3 A); and the ABT-325 Fab (1.5 A). These structures, along with human/mouse IL-18 chimera binding data, allow us to make three key observations relevant to the biology and antigenic recognition of IL-18 and related cytokines. First, several IL-18 residues shift dramatically (> 10 A) upon binding 125-2H, compared with unbound IL-18 (Kato, Z., Jee, J., Shikano, H., Mishima, M., Ohki, I., Ohnishi, H., Li, A., Hashimoto, K., Matsukuma, E., Omoya, K., Yamamoto, Y., Yoneda, T., Hara, T., Kondo, N., and Shirakawa, M. (2003) Nat. Struct. Biol. 10, 966-971). IL-18 thus exhibits plasticity that may be common to its interactions with other receptors. Related cytokines may exhibit similar plasticity. Second, ABT-325 and 125-2H differ significantly in combining site character and architecture, thus explaining their ability to bind IL-18 simultaneously at distinct epitopes. These data allow us to define the likely ABT-325 epitope and thereby explain the distinct neutralizing mechanisms of both antibodies. Third, given the high 125-2H potency, 10 well ordered water molecules are trapped upon complex formation in a cavity between two IL-18 loops and all six 125-2H complementarity-determining regions. Thus, counterintuitively, tight and specific antibody binding may in some cases be water-mediated.

Selected figure(s)

Figure 2.
125-2H binds human IL-18 residue Leu^180 in a deep pocket, trapping 10 water molecules. a, overview of the complex. The antibody engages the primary (Leu^180) and secondary (Pro^143) IL-18 loops. IL-18 is colored as a rainbow, from the NH[2] to the COOH terminus; CDRs 1, 2, and 3 of the 125-2H Fab fragment (purple, heavy chain; pink, light chain) are colored orange, yellow, and green, with the heavy chain in darker tones. The solvent-inaccessible, water-filled cavity trapped between 125-2H Fab and IL-18 is shown (brown dots). b, the center of the combining site, viewed from the perspective of IL-18 (gray). Note the deep hydrophobic pocket, formed by heavy and light chain Tyr and Leu residues, that binds Leu^180. c, the periphery of the combining site is ringed by charge-charge and hydrogen bonding interactions involving all six 125-2H CDRs. d, stereoview illustrating the large cavity (brown dots) formed between the IL-18 primary and secondary loops and the 125-2H CDRs, trapping 10 well ordered water molecules. The detailed hydrogen bond interactions are shown in supplemental Fig. 2.

Figure 6.
Multiple IL-18 epitopes mediate binding to multiple receptors. IL-18Rα and IL-18BP were modeled based on the IL-1R1 crystal structure (13) (Protein Data Bank entry 1ITB) and are shown bound to IL-18. a, engagement of IL-18 (gray) by IL-18Rα completely blocks the proposed ABT-325 epitope (magenta), and β-strands B and D (red) in domain 2 collide with 125-2H CDR H2. The IL-18BP (red) and IL-18Rβ (green; “Site 3” (see Ref. 1)) epitopes are also shown. b, close up view of the collision between 125-2H and IL-18Rα, viewed from behind relative to a. c, 125-2H, ABT-325, and IL-18BP can all bind IL-18 simultaneously, since their epitopes do not overlap.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 24478-24489) copyright 2009.

Figures were selected by an automated process.