PDBsum entry 3b2u

Immune system/transferase

PDB id: 3b2u

Contents

Protein chains

(+ 2 more) 213 a.a. *

(+ 2 more) 217 a.a. *

(+ 2 more) 195 a.a. *

Ligands

NAG-NAG-BMA-MAN ×3

NAG-NAG ×7

NAG-NAG-BMA ×7

NAG-NAG-BMA-MAN-MAN

NAG ×14

SO4 ×8

Waters ×1036

* Residue conservation analysis

PDB id:

3b2u

Name:

Immune system/transferase

Title:

Crystal structure of isolated domain iii of the extracellular region of the epidermal growth factor receptor in complex with the fab fragment of imc-11f8

Structure:

Imc-11f8 fab light chain. Chain: l, d, g, k, o, r, u, x. Engineered: yes. Imc-11f8 fab heavy chain. Chain: h, c, f, j, n, q, t, w. Engineered: yes. Epidermal growth factor receptor. Chain: a, b, e, i, m, p, s, v. Fragment: sequence database residues 335-538.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: egfr. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expressed in: mus musculus. Expression_system_taxid: 10090. Gene: egfr, erbb1.

Resolution:

2.58Å R-factor: 0.230 R-free: 0.291

Authors:

K.M.Ferguson,S.Li,P.Kussie

Key ref:

S.Li et al. (2008). Structural basis for EGF receptor inhibition by the therapeutic antibody IMC-11F8. Structure, 16, 216-227. PubMed id: 18275813 DOI: 10.1016/j.str.2007.11.009

Date:

19-Oct-07 Release date: 19-Feb-08

Protein chains

No UniProt id for this chain

Struc: 213 a.a.

Protein chains

Q6GMX6  (Q6GMX6_HUMAN) -  IGH@ protein from Homo sapiens

Seq: 465 a.a.

Struc: 217 a.a.*

Protein chains

P00533  (EGFR_HUMAN) -  Epidermal growth factor receptor from Homo sapiens

Seq: 1210 a.a.

Struc: 195 a.a.*

* PDB and UniProt seqs differ at 19 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, E, I, M, P, S, V: E.C.2.7.10.1 - receptor protein-tyrosine kinase.
• Reaction: L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H⁺

L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] (Bound ligand (Het Group name = NAG) matches with 41.38% similarity) + ADP + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.str.2007.11.009

Structure 16:216-227 (2008)

PubMed id: 18275813

Structural basis for EGF receptor inhibition by the therapeutic antibody IMC-11F8.

S.Li, P.Kussie, K.M.Ferguson.

ABSTRACT

Therapeutic anticancer strategies that target and inactivate the epidermal growth factor receptor (EGFR) are under intense study in the clinic. Here we describe the mechanism of EGFR inhibition by an antibody drug IMC-11F8. IMC-11F8 is a fully human antibody that has similar antitumor potency as the chimeric cetuximab/Erbitux and might represent a safer therapeutic alternative. We report the X-ray crystal structure of the Fab fragment of IMC-11F8 (Fab11F8) in complex with the entire extracellular region and with isolated domain III of EGFR. We compare this to our previous study of the cetuximab/EGFR interaction. Fab11F8 interacts with a remarkably similar epitope, but through a completely different set of interactions. Both the similarities and differences in binding of these two antibodies have important implications for the development of inhibitors that could exploit this same mechanism of EGFR inhibition.

Selected figure(s)

Figure 4.
Figure 4. Features of the Shared Fab11F8, FabC225, and EGF Binding Region on Domain III
(A) Molecular surface representations of domain III of sEGFR with the contact regions (as defined in Figure 3D) colored red for Fab11F8, yellow for FabC225, and blue for EGF. Orientation is looking down onto the domain III binding site.
(B) Functional features of the domain III molecular surface. In the left panel, the surface is colored by atom type: negative, red; positive, blue; polar oxygen, pink; polar nitrogen, light blue; and apolar, white. The right panel shows the electrostatic potential from −2.5 kT (red) to +2.5 kT (blue) projected onto the surface. Electrostatic potential calculations used the adaptive Poisson-Boltzmann solver (APBS) implemented in PyMOL ([Baker et al., 2001] and [DeLano, 2004]).
(C) Orthogonal views of domain III. High-mannose chains (yellow) have been placed at each position of glycosylation on sEGFR guided by the one or two ordered sugar groups that are seen in the X-ray crystal structures. For reference, the contact region of Fab11F8 is shown (red).
(D) Three orientations of sEGFR are shown with the electrostatic potential, as in (B), projected on the surface and high-mannose chains shown. Both electrostatic and carbohydrate steering might play a role in guiding Fabs or ligands to the shared binding site on domain III.

Figure 8.
Figure 8. Mechanism of Inhibition of EGFR Activation by IMC-11F8 and by Cetuximab
(A) Cartoon model of Fab11F8 bound to sEGFR colored as in Figure 3A. Domain I and the N-terminal portion of domain II (gray) have been modeled using the coordinates from PDB ID code 1YY9.
(B) Cartoon of the FabC225/sEGFR complex (PDB ID code: 1YY9) colored as in (A).
(C) The mechanism of inhibition of ligand-induced dimerization and activation of EGFR for IMC-11F8 and cetuximab based on the structures presented here and in Li et al. (2005). The binding of the antibody to domain III of EGFR prevents ligand binding and might also sterically inhibit the conformational change that must occur for dimerization.

The above figures are reprinted by permission from Cell Press: Structure (2008, 16, 216-227) copyright 2008.

Figures were selected by an automated process.