PDBsum entry 3c09

Immune system/transferase

PDB id: 3c09

Contents

Protein chains

211 a.a.

216 a.a.

191 a.a.

175 a.a.

191 a.a.

Ligands

NAG ×10

BMA ×2

MAN

References listed in PDB file

Key reference

Title

Matuzumab binding to egfr prevents the conformational rearrangement required for dimerization.

Authors

J.Schmiedel, A.Blaukat, S.Li, T.Knöchel, K.M.Ferguson.

Ref.

Cancer Cell, 2008, 13, 365-373. [DOI no: 10.1016/j.ccr.2008.02.019]

PubMed id

18394559

Abstract

An increasing number of therapeutic antibodies targeting tumors that express the epidermal growth factor receptor (EGFR) are in clinical use or late stages of clinical development. Here we investigate the molecular basis for inhibition of EGFR activation by the therapeutic antibody matuzumab (EMD72000). We describe the X-ray crystal structure of the Fab fragment of matuzumab (Fab72000) in complex with isolated domain III from the extracellular region of EGFR. Fab72000 interacts with an epitope on EGFR that is distinct from the ligand-binding region on domain III and from the cetuximab/Erbitux epitope. Matuzumab blocks ligand-induced receptor activation indirectly by sterically preventing the domain rearrangement and local conformational changes that must occur for high-affinity ligand binding and receptor dimerization.

Figure 5.
Figure 5. Implications for the Mechanism of Inhibition of EGFR by Matuzumab
(A) Cartoon of the extended sEGFR with Fab72000, in surface representation, docked onto its domain III epitope. The orientation of the receptor is the same as for the right-hand protomer in the sEGFR dimer shown in Figure 1 (with domains colored as for the left-hand protomer; EGF is omitted for clarity). The Fab72000 is colored as in Figure 3. The N-terminal region of domain I clashes with the V[L] domain (indicated with an arrow). Additional clashes occur along the C-terminal half of domain II (see [B]). The C-terminal loop on domain II (D278, H280) that makes critical contacts across the dimer interface is marked with an asterisk.
(B) In this view, an approximate 50° rotation about the vertical axis relative to (A), domain II is shown in sphere representation in dark green. A cartoon of domain II of the other molecule in the dimer is shown (light green) for reference. Domain I has been omitted for clarity. The V[L] domain of the Fab clashes with domain II in the critical C-terminal region that forms the binding pocket for the dimerization arm and makes important contacts with domain III (from N274 and E293 in domain II, colored orange). These interactions are known to be crucial for stabilizing the dimerization competent conformation of domain II. The Fab72000 epitope loop on domain III is colored in red.

Figure 7.
Figure 7. Matuzumab and Cetuximab Use Different Mechanisms to Block Ligand-Induced EGFR Dimerization and Activation
In the center of the scheme, the ligand-induced sEGFR dimer is represented, with domain I in red, domain II in green, domain III in gray with red border, domain IV in gray with green border, and the ligand (E) in violet. The colors for one protomer are lightened for contrast. On the left-hand side a scheme is shown to illustrate the mechanism of inhibition of ligand-induced dimerization by matuzumab. Fab72000 binds to domain III of sEGFR and sterically prevents the receptor from adopting the conformation required for dimerization. Importantly, Fab72000 blocks the local conformational changes in domain II that are critical for both high-affinity ligand binding and dimerization. The inhibition is noncompetitive; the ligand-binding site on domain III is not blocked. This contrasts with the mechanism of inhibition previously reported for cetuximab (Li et al., 2005). FabC225 (right side) is a competitive inhibitor that blocks the ligand-binding site on domain III. This is the primary mechanism of inhibition of ligand-mediated dimerization by cetuximab.

The above figures are reprinted from an Open Access publication published by Cell Press: Cancer Cell (2008, 13, 365-373) copyright 2008.