Canonical features of human antibodies recognizing the influenza hemagglutinin trimer interface
Seth J. Zost, … , Andrew B. Ward, James E. Crowe Jr.
Seth J. Zost, … , Andrew B. Ward, James E. Crowe Jr.
Published June 22, 2021
Citation Information: J Clin Invest. 2021;131(15):e146791. https://doi.org/10.1172/JCI146791.
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Research Article Immunology

Canonical features of human antibodies recognizing the influenza hemagglutinin trimer interface

Abstract

Broadly reactive antibodies targeting the influenza A virus hemagglutinin (HA) head domain are thought to be rare and to require extensive somatic mutations or unusual structural features to achieve breadth against divergent HA subtypes. Here we describe common genetic and structural features of protective human antibodies from several individuals recognizing the trimer interface (TI) of the influenza A HA head, a recently identified site of vulnerability. We examined the sequence of TI-reactive antibodies, determined crystal structures for TI antibody–antigen complexes, and analyzed the contact residues of the antibodies on HA to discover common genetic and structural features of TI antibodies. Our data reveal that many TI antibodies are encoded by a light chain variable gene segment incorporating a shared somatic mutation. In addition, these antibodies have a shared acidic residue in the heavy chain despite originating from diverse heavy chain variable gene segments. These studies show that the TI region of influenza A HA is a major antigenic site with conserved structural features that are recognized by a common human B cell public clonotype. The canonical nature of this antibody–antigen interaction suggests that the TI epitope might serve as an important target for structure-based vaccine design.

Authors

Seth J. Zost, Jinhui Dong, Iuliia M. Gilchuk, Pavlo Gilchuk, Natalie J. Thornburg, Sandhya Bangaru, Nurgun Kose, Jessica A. Finn, Robin Bombardi, Cinque Soto, Elaine C. Chen, Rachel S. Nargi, Rachel E. Sutton, Ryan P. Irving, Naveenchandra Suryadevara, Jonna B. Westover, Robert H. Carnahan, Hannah L. Turner, Sheng Li, Andrew B. Ward, James E. Crowe Jr.

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Figure 2

Structural and functional characterization of mAb H5.28 and H5.31 binding to HA.

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Structural and functional characterization of mAb H5.28 and H5.31 bindin...
(A) HDX-MS with H5.28 Fab and H5 HA head domain identified a putative epitope for H5.28 at the TI. The amino acid sequence of the H5 head domain is shown with a ribbon diagram indicating differences in deuterium uptake. Blue colors indicate slower deuterium exchange in the presence of H5.28 Fab, while red colors indicate faster deuterium exchange in the presence of H5.28 Fab. Data are shown for 10 seconds, 100 seconds, and 1000 seconds of deuterium labeling. The 3 major peptides are colored blue on an H5 trimer. (B) Selected 2D class averages of H1 HA trimer (A/California/04/2009) alone or after a 20-second incubation with H5.28 (middle) or H5.31 Fab (right). All of the Fabs complexed with HA were in monomeric form, while a few apo HA trimers were observed. Below is a cartoon illustration showing that H5.28 or H5.31 Fab (magenta) results in dissociation of recombinantly expressed HA trimer (gray/blue/lavender), as visualized in the negative-stain EM data. (C) H5.28 and H5.31 preferentially bound to uncleaved HA expressed on the cell surface. In contrast, a recombinant form of the stem mAb FI6v3 preferentially bound to cleaved HA. P values for the comparison between binding to cleaved and uncleaved HA were computed using an unpaired 2-way Student’s t test. (D) Crystal structure of H5.31 in complex with VN/04 HA. H5.31 heavy chain is colored in gold, the light chain in cyan, and H5 head domain in dark gray. A glycosylation site on H5.31, N74 on the H5.31 DE loop, is labeled and shown as sticks, and 2 fitted NAG residues of the glycan are shown also as sticks. The 220 loop of the VN/04 HA head domain is labeled, and the receptor binding site is highlighted with a red circle. (E) Crystal structure of H5.28 in complex with VN/04 HA. H5.28 heavy chain is colored in salmon, the light chain in lavender, and H5 HA head domain in light gray. (F) Superimposition of the 2 complex structures. Structural variations can be seen at HCDR1s, HCDR2s, and heavy chain DE loops. (G) The HA epitope recognized by H5.31 is mapped onto the surface of one protomer of the VN/04 HA trimer. The mapped protomer is colored dark gray, the 220 loop in purple, and the 90 loop in orange. The other 2 protomers are colored in light gray and blue, respectively. (H and I) Structural details of the H5.31/VN/04-HA complex. (H) Interactions of H5.31 with 220 loop of the HA head domain, with the HCDR3 E98/LCDR2 Y49 interaction shown with blue dashes. Relevant residues of the HA head domain are labeled in purple, those of the heavy chain in red, and those of the light chain in blue. (I) Interactions of H5.31 HCDR3 with 90 loop and its C-terminal β strand. Relevant residues of the HA head domain are labeled in orange, those of the heavy chain in red, and those of the light chain in blue.