Structure of a classical broadly neutralizing stem antibody in complex with a pandemic H2 influenza virus hemagglutinin

Abstract

We report the structural characterization of the first antibody identified to cross-neutralize multiple subtypes of influenza A viruses. The crystal structure of mouse antibody C179 bound to the pandemic 1957 H2N2 hemagglutinin (HA) reveals that it targets an epitope on the HA stem similar to those targeted by the recently identified human broadly neutralizing antibodies. C179 also inhibits the low-pH conformational change of the HA but uses a different angle of approach and both heavy and light chains.

Fig 1

In vitro binding and neutralization mechanism of C179. (A) Phylogenetic tree showing the relationships between the 17 HA subtypes of influenza A virus, divided into two major lineages (groups 1 and 2). C179 binds multiple group 1 subtypes (orange text). Subtypes neutralized by the other stem bnAbs are denoted. The phylogenetic distance to influenza B virus is not to scale. *, HA not tested for binding. (B) C179 inhibits the HA pH-induced conformational change that drives membrane fusion. Exposure to low pH converts Jap57/H2 HA to a postfusion state that is sensitive to trypsin digestion (lane 1). Preincubation with C179 prevents this conversion, retaining the HA in the protease-resistant, prefusion form (lane 2).

Fig 2

C179 binds an epitope in the HA stem. (A) Crystal structure of Jap57/H2 in complex with the Fab from mouse monoclonal antibody C179 (PDB ID no. 4HLZ). One HA/Fab protomer of the trimeric complex is colored with HA1 in green, HA2 in light blue, Fab heavy chain in magenta, Fab light chain in orange, and N-linked glycans as spheres colored by atom type. The two other protomers are colored in gray. (B) Footprint of C179 on the HA highlighting HA residues interacting with C179 with HA1 residues in green and HA2 residues in light blue. (C) Footprint of HA on C179 with the heavy chain interacting surfaces in magenta and the light chain interacting surfaces in orange; Fab residues contacting the HA are labeled.

Fig 3

C179 interactions with Jap57/H2 HA and comparison with FI6 and CR9114. (A) Surface representation of the C179 epitope on the HA stem with side chains of interacting residues from C179 shown and colored by CDR loop. HCDR1, pink; HCDR3, brown; LCDR1, green; LCDR2, orange. (B and C) Similar representation of FI6 (V_H3-30) and CR9114 (V_H1-69) in complex with H1 HA (PDB 3ZTN) and H5 HA (PDB 4FQI), respectively. Colors are as described for panel A, with HCDR2 in purple and FR3 in cyan.