2OR9

The structure of the anti-c-myc antibody 9E10 Fab fragment/epitope peptide complex reveals a novel binding mode dominated by the heavy chain hypervariable loops

Summary for 2OR9

• Entry DOI: 10.2210/pdb2or9/pdb
• Related: 2ORB
• Descriptor: Monoclonal anti-c-myc antibody 9E10, synthetic epitope peptide of 9E10, ... (4 entities in total)
• Functional Keywords: antigen-antibody complex, antigen recognition, myc-tag, long cdr h3, immune system
• Biological source: Mus musculus (house mouse); More
• Total number of polymer chains: 5
• Total formula weight: 99121.09

Authors

Krauss, N.,Scheerer, P.,Hoehne, W. (deposition date: 2007-02-02, release date: 2008-02-12, Last modification date: 2023-08-30)

Primary citation

Krauss, N.,Wessner, H.,Welfle, K.,Welfle, H.,Scholz, C.,Seifert, M.,Zubow, K.,Ay, J.,Hahn, M.,Scheerer, P.,Skerra, A.,Hohne, W.
The structure of the anti-c-myc antibody 9E10 Fab fragment/epitope peptide complex reveals a novel binding mode dominated by the heavy chain hypervariable loops.
Proteins, 73:552-565, 2008

PubMed Abstract: The X-ray structure of the Fab fragment from the anti-c-myc antibody 9E10 was determined both as complex with its epitope peptide and for the free Fab. In the complex, two Fab molecules adopt an unusual head to head orientation with the epitope peptide arranged between them. In contrast, the free Fab forms a dimer with different orientation. In the Fab/peptide complex the peptide is bound to one of the two Fabs at the "back" of its extended CDR H3, in a cleft with CDR H1, thus forming a short, three-stranded antiparallel beta-sheet. The N- and C-terminal parts of the peptide are also in contact with the neighboring Fab fragment. Comparison between the CDR H3s of the two Fab molecules in complex with the peptide and those from the free Fab reveals high flexibility of this loop. This structural feature is in line with thermodynamic data from isothermic titration calorimetry.

PubMed: 18473392
DOI: 10.1002/prot.22080

Experimental method

X-RAY DIFFRACTION (2.7 Å)