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A recurring motif for antibody recognition of the receptor-binding site of influenza hemagglutinin

Abstract

Influenza virus hemagglutinin (HA) mediates receptor binding and viral entry during influenza infection. The development of receptor analogs as viral-entry blockers has not been successful, which suggests that sialic acid may not be an ideal scaffold to obtain broad, potent HA inhibitors. Here, we report crystal structures of Fab fragments from three human antibodies that neutralize the 1957 pandemic H2N2 influenza virus in complex with H2 HA. All three antibodies use an aromatic residue to plug a conserved cavity in the HA receptor-binding site. Each antibody interacts with the absolutely conserved HA1 Trp153 at the cavity base through π-π stacking with the signature Phe54 of two VH1-69–encoded antibodies or a tyrosine from HCDR3 in the other antibody. This highly conserved interaction can be used as a starting point to design inhibitors targeting this conserved hydrophobic pocket in influenza viruses.

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Figure 1: Structures of H2 HA–VH1-69 antibody complexes.
Figure 2: Antibody-antigen binding footprints in the 2G1 and 8M2 complexes.
Figure 3: Antibody-antigen interactions in the 2G1 and 8M2 complexes.
Figure 4: Crystal structure of 8F8 with H2 HA.
Figure 5: Antibody-antigen recognition by 8F8.
Figure 6: Escape mutations on H2 HA for binding to antibodies 8F8, 8M2 and 2G1 and their effects on binding of glycan receptors.
Figure 7: Targeting the receptor-binding site.

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Acknowledgements

The work was supported in part by US National Institutes of Health (NIH) grants AI058113 (I.A.W., J.E.C. and J.C.P.) and R01 AI106002 (J.E.C.), US Department of Defense grant HDTRA1-08-10-BRCWMD-BAA and NIH contract HHSN272200900047C (J.E.C.), the Skaggs Institute for Chemical Biology, the Scripps Microarray Core Facility and a contract from the US Centers for Disease Control and Prevention (J.C.P.). Glycans used for HA binding assay were partially provided by the Consortium for Functional Glycomics (http://www.functionalglycomics.org/) funded by US National Institute of General Medical Sciences (NIGMS) grant GM62116 (J.C.P.). We thank W. Yu and X. Dai (Scripps Research Institute) for excellent technical support. This is publication 21487 from The Scripps Research Institute.

X-ray diffraction data sets were collected at the Advanced Photon Source beamline 23ID-B (GM/CA CAT) and the Stanford Synchrotron Radiation Lightsource beamline 12-2. GM/CA CAT has been funded in whole or in part with federal funds from the US National Cancer Institute (Y1-CO-1020) and the NIGMS (Y1-GM-1104). Use of the Advanced Photon Source was supported by the US Department of Energy (DOE), Basic Energy Sciences, Office of Science, under contract No. DE-AC02-06CH11357. The Stanford Synchrotron Radiation Lightsource is a Directorate of SLAC National Accelerator Laboratory and an Office of Science User Facility operated for the DOE Office of Science by Stanford University. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research and by the NIH, NIGMS (including P41GM103393) and the National Center for Research Resources (NCRR; P41RR001209). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS, NCRR or NIH.

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R.X., J.C.K., J.E.C. and I.A.W. designed the research; R.X., J.C.K. and R.M. performed the research; R.X., J.C.K., R.M., J.C.P., J.E.C. and I.A.W. analyzed data; J.E.C. and I.A.W. supervised the project; and R.X., J.C.K., J.E.C. and I.A.W. wrote the manuscript.

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Correspondence to James E Crowe Jr or Ian A Wilson.

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Vanderbilt University previously submitted a patent application (with J.C.K. and J.E.C. named on the patent application) covering the diagnostic and therapeutic use of antibodies 2G1, 8M2 and 8F8 prior to the structural work described here.

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Xu, R., Krause, J., McBride, R. et al. A recurring motif for antibody recognition of the receptor-binding site of influenza hemagglutinin. Nat Struct Mol Biol 20, 363–370 (2013). https://doi.org/10.1038/nsmb.2500

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