4NKI

Crystal structure of a Fab

Summary for 4NKI

• Entry DOI: 10.2210/pdb4nki/pdb
• Descriptor: Fab light chain, Fab heavy chain, 1,2-ETHANEDIOL, ... (4 entities in total)
• Functional Keywords: nonoclonal antibody, immunoglobulin, antibody, pd-l1, soluble protein, cytokine
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 47636.06

Authors

Jiang, X. (deposition date: 2013-11-12, release date: 2014-11-12, Last modification date: 2024-11-06)

Primary citation

Hao, G.,Wesolowski, J.S.,Jiang, X.,Lauder, S.,Sood, V.D.
Epitope characterization of an anti-PD-L1 antibody using orthogonal approaches.
J.Mol.Recognit., 28:269-276, 2015

PubMed Abstract: The binding of programmed death ligand 1 protein (PD-L1) to its receptor programmed death protein 1 (PD-1) mediates immunoevasion in cancer and chronic viral infections, presenting an important target for therapeutic intervention. Several monoclonal antibodies targeting the PD-L1/PD-1 signaling axis are undergoing clinical trials; however, the epitopes of these antibodies have not been described. We have combined orthogonal approaches to localize and characterize the epitope of a monoclonal antibody directed against PD-L1 at good resolution and with high confidence. Limited proteolysis and mass spectrometry were applied to reveal that the epitope resides in the first immunoglobulin domain of PD-L1. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) was used to identify a conformational epitope comprised of discontinuous strands that fold to form a beta sheet in the native structure. This beta sheet presents an epitope surface that significantly overlaps with the PD-1 binding interface, consistent with a desired PD-1 competitive mechanism of action for the antibody. Surface plasmon resonance screening of mutant PD-L1 variants confirmed that the region identified by HDX-MS is critical for the antibody interaction and further defined specific residues contributing to the binding energy. Taken together, the results are consistent with the observed inhibitory activity of the antibody on PD-L1-mediated immune evasion. This is the first report of an epitope for any antibody targeting PD-L1 and demonstrates the power of combining orthogonal epitope mapping techniques.

PubMed: 25664688
DOI: 10.1002/jmr.2418

Experimental method

X-RAY DIFFRACTION (2.41 Å)