A neutralizing human antibody induces movement of the HCoV-229E receptor binding domain

Figures

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  Fig. 1. Isolation and characterization of HCoV-229E RBD-SD1-specific human antibodies. A A FACS dot plot of IgD- B cells is shown, with cells stained using HCoV-229E RBD-SD1 conjugated to two different fluorochromes. B BLI sensorgrams measuring binding interactions for DH1532 (left) and DH1533 (right) to HCoV-229E RBD-SD1. Data are shown as black lines and 1:1 binding model fits are shown as red lines. The corresponding kinetic values for each interaction are shown below. The displayed sensorgrams are representative curves from a single experiment but binding experiments were performed in duplicate and all data were used to calculate the kinetic values. C Cartoon depicting BLI-based receptor competition assay. Biosensors loaded with HCoV-229E RBD-SD1 were first dipped into wells containing IgG before being transferred to a well containing both IgG and soluble APN ectodomain. D Sensorgram showing results of receptor competition assay. The yellow biosensor was dipped into DH1532 during the first phase. The purple biosensor was dipped into DH1533 during the first phase. The blue biosensor was dipped into buffer alone during the first phase. All biosensors were then transferred to wells…

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  Fig. 2. Strain-specific neutralization of HCoV-229E reporter viruses. Antibody neutralization activity against A icVR-740 and B icUNC/2/2022 reporter viruses. DH1532 is colored yellow, DH1533 is colored purple and the mixture of DH1532 and DH1533 is colored gray. IC50 values for each antibody are labeled in the corresponding colors. Each point represents a single technical replicate (n = 2).

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  Fig. 3. Viral sequence diversity in the RBD impacts DH1533 binding. A Sequence variability has been mapped onto the structure of the HCoV-229E RBD (PDB ID: 6U7G) using ConSurf. More conserved residues are colored purple and less conserved residues are colored teal. B Sequence identity of the RBD relative to the BN1/GER/2015 strain is plotted for representative HCoV-229E variants spanning 1962–2022. Time separating 2015 from the year when a strain was isolated is plotted on the x-axis. The red dashed line shows a linear regression, with an R2 value of 0.9417. C BLI sensorgrams are shown, measuring binding of 10 nM DH1532 Fab (left) and 10 nM DH1533 Fab (right) to HCoV-229E RBD-SD1 constructs from representative strains isolated between 1984 and 2022. Full concentration series for each of these interactions can be found in Supplementary Fig. 4.

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  Fig. 4. The cryo-EM structure of DH1533 bound to HCoV-229E S. A The structure of DH1533-bound HCoV-229E S2P is shown as ribbon diagrams, docked into the transparent cryo-EM map from ”side” (left) and “top” (right) views. HCoV-229E S2P is colored green, the DH1533 heavy chain is colored purple and the DH1533 light chain is colored white. B A single DH1533-bound RBD is shown for the sake of clarity from a “top” view, surrounded by a cutout of the corresponding cryo-EM map. C An individual DH1533-bound RBD is shown in ribbon diagrams, with the APN ectodomain from a previously determined co-crystal structure (PDB ID: 6U7G), shown as a a blue, transparent molecular surface docked into the bound conformation relative to the HCoV-229E RBD. D A zoomed-in view of the DH1533 binding interface from the “top” view is shown. Chains are colored according to panel A and critical contact residues are shown as sticks. Oxygen atoms are colored red, nitrogen atoms are colored blue and predicted hydrogen bonds are shown as black dashed lines. E An additional view of the DH1533 binding interface is shown, rotated 200° relative to (D).

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  Fig. 5. DH1533 binding induces RBD movement in neighboring, unbound protomers. A Top and B side views of the three cryo-EM reconstructions that were calculated from the DH1533 Fab + HCoV-229E S2P dataset are shown. The portions of each map corresponding to the RBDs have been colored green and the portions corresponding to DH1533 have been colored purple.