5AZ2

Crystal structure of the Fab fragment of 9E5, a murine monoclonal antibody specific for human epiregulin

Summary for 5AZ2

• Entry DOI: 10.2210/pdb5az2/pdb
• Descriptor: anti-human epiregulin antibody 9E5 Fab heavy chain, anti-human epiregulin antibody 9E5 Fab light chain (3 entities in total)
• Functional Keywords: antibody, immunoglobulin, monoclonal antibody, epidermal growth factor, immune system
• Biological source: Mus musculus; More
• Total number of polymer chains: 2
• Total formula weight: 47294.72

Authors

Kado, Y.,Mizohata, E.,Nagatoishi, S.,Iijima, M.,Shinoda, K.,Miyafusa, T.,Nakayama, T.,Yoshizumi, T.,Sugiyama, A.,Kawamura, T.,Lee, Y.H.,Matsumura, H.,Doi, H.,Fujitani, H.,Kodama, T.,Shibasaki, Y.,Tsumoto, K.,Inoue, T. (deposition date: 2015-09-16, release date: 2015-12-09, Last modification date: 2020-02-26)

Primary citation

Kado, Y.,Mizohata, E.,Nagatoishi, S.,Iijima, M.,Shinoda, K.,Miyafusa, T.,Nakayama, T.,Yoshizumi, T.,Sugiyama, A.,Kawamura, T.,Lee, Y.H.,Matsumura, H.,Doi, H.,Fujitani, H.,Kodama, T.,Shibasaki, Y.,Tsumoto, K.,Inoue, T.
Epiregulin Recognition Mechanisms by Anti-epiregulin Antibody 9E5: STRUCTURAL, FUNCTIONAL, AND MOLECULAR DYNAMICS SIMULATION ANALYSES
J.Biol.Chem., 291:2319-2330, 2016

PubMed Abstract: Epiregulin (EPR) is a ligand of the epidermal growth factor (EGF) family that upon binding to its epidermal growth factor receptor (EGFR) stimulates proliferative signaling, especially in colon cancer cells. Here, we describe the three-dimensional structure of the EPR antibody (the 9E5(Fab) fragment) in the presence and absence of EPR. Among the six complementarity-determining regions (CDRs), CDR1-3 in the light chain and CDR2 in the heavy chain predominantly recognize EPR. In particular, CDR3 in the heavy chain dramatically moves with cis-trans isomerization of Pro(103). A molecular dynamics simulation and mutational analyses revealed that Arg(40) in EPR is a key residue for the specific binding of 9E5 IgG. From isothermal titration calorimetry analysis, the dissociation constant was determined to be 6.5 nm. Surface plasmon resonance analysis revealed that the dissociation rate of 9E5 IgG is extremely slow. The superimposed structure of 9E5(Fab)·EPR on the known complex structure of EGF·EGFR showed that the 9E5(Fab) paratope overlaps with Domains I and III on the EGFR, which reveals that the 9E5(Fab)·EPR complex could not bind to the EGFR. The 9E5 antibody will also be useful in medicine as a neutralizing antibody specific for colon cancer.

PubMed: 26627827
DOI: 10.1074/jbc.M115.656009

Experimental method

X-RAY DIFFRACTION (1.603 Å)