Supplementary data from: Assessing the structural boundaries of broadly reactive antibody interactions with diverse H3 influenza hemagglutinin proteins
Data files
Sep 15, 2025 version files 226.79 MB
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Dryad_Deposition.zip
226.78 MB
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README.md
7.75 KB
Abstract
Influenza virus infections are an ongoing seasonal disease burden and persistent pandemic threat. Vaccine antigens that can elicit or recall broadly neutralizing antibodies are a high priority for the development of next-generation influenza vaccines to reduce the impact of antigenic drift on vaccine efficacy. Ideally, broadly neutralizing antibodies should be resilient to changes in viral antigens over time. This dataset contains raw and processed biolayer interferometry data of the binding characteristics of three antibodies (TJ5-1, TJ5-13, and #1664) with influenza H3 antigens representing almost 50 years of virus evolution. In addition, AlphaFold3 generated models of the A/Tasmania/503/2020 HA are included in the absence of publicly available models of related H3 structures.
https://doi.org/10.5061/dryad.tmpg4f57v
Description of the data and file structure
Supplemental data for the manuscript "Assessing the structural boundaries of broadly reactive antibody interactions with diverse H3 influenza hemagglutinin proteins". Raw and processed data are included from biolayer interferometry experiments of broadly neutralizing antibodies against a diverse range of hemagglutinin proteins derived from H3N2 viruses. Correspondence should be addressed to Rebecca DuBois (rmdubois@ucsc.edu).
Files and variables
File: Dryad_Deposition.zip
Description: Compressed archive containing manuscript supplemental data.
Folder: Raw_Data
Description: Folder containing Microsoft Excel files with raw data for biolayer interferometry (BLI) experiments.
- File: 1664_mAb_BLI_raw.xlsx
- Description: Microsoft Excel notebook containing raw BLI data exported from Octet Data Analysis HT software v7 for IgG #1664 binding with recombinant influenza H3N2 hemagglutinin (HA) proteins. Units of time are in seconds. Concentrations are expressed as nanomolar (nM). The data is organized in tabs for each HA with plate well numbers and associated concentrations organized by columns in each sheet.
- File: TJ5-1_mAb_BLI_raw.xlsx
- Description: Microsoft Excel notebook containing raw BLI data exported from Octet Data Analysis HT software v7 for IgG TJ5-1 binding with recombinant influenza H3N2 hemagglutinin (HA) proteins. Units of time are in seconds. Concentrations are expressed as nanomolar (nM). The data is organized in tabs for each HA with plate well numbers and associated concentrations organized by columns in each sheet.
- File: TJ5-1_mAb_BLI_raw.xlsx
- Description: Microsoft Excel notebook containing raw BLI data exported from Octet Data Analysis HT software v7 for IgG TJ5-13 binding with recombinant influenza H3N2 hemagglutinin (HA) proteins. Units of time are in seconds. Concentrations are expressed as nanomolar (nM). The data is organized in tabs for each HA with plate well numbers and associated concentrations organized by columns in each sheet.
Folder: Processed_BLI_data
Description: Folder containing Microsoft Excel files with raw data for biolayer interferometry (BLI) experiments.
- File: 1664_mAb_BLI_processed.xlsx
- Description: Microsoft Excel notebook containing processed BLI data (association and dissociation phases) exported from Octet Data Analysis HT software v7 for IgG #1664 binding with recombinant influenza H3N2 hemagglutinin (HA) proteins. Units of time are in seconds relative to the beginning of the experiment. Concentrations are expressed as nanomolar (nM). The data is organized in tabs for each HA with plate well numbers and associated concentrations organized by columns in each sheet.
- File: TJ5-1_mAb_BLI_processed.xlsx
- Description: Microsoft Excel notebook containing processed BLI data (association and dissociation phases) exported from Octet Data Analysis HT software v7 for IgG TJ5-1 binding with recombinant influenza H3N2 hemagglutinin (HA) proteins. Units of time are in seconds relative to the beginning of the experiment. Concentrations are expressed as nanomolar (nM). The data is organized in tabs for each HA with plate well numbers and associated concentrations organized by columns in each sheet.
- File: TJ5-13_mAb_BLI_processed.xlsx
- Description: Microsoft Excel notebook containing processed BLI data (association and dissociation phases) exported from Octet Data Analysis HT software v7 for IgG TJ5-13 binding with recombinant influenza H3N2 hemagglutinin (HA) proteins. Units of time are in seconds relative to the beginning of the experiment. Concentrations are expressed as nanomolar (nM). The data is organized in tabs for each HA with plate well numbers and associated concentrations organized by columns in each sheet.
- File: Detailed_Kinetics_Tables
- Excel notebook containing the full kinetics tables for each antibody-HA experiment.
- Sensor Location: position of the biosensor in the instrument.
- Sensor Type: the functionalized biosensor type used for the assay.
- Baseline Loc.: the well position in the plate used for the Baseline step during the assay.
- Assoc. (Sample) Loc.: the well position in the plate used for the Association step during the assay.
- Sample ID: the user-provided name of the sample contained in the well used for the Association step.
- Dissoc. Loc.: the well position in the plate used for the Dissociation step during the assay.
- Loading Loc.: the well position in the plate used for the Loading step during the assay.
- Loading Sample ID: the user-provided name of the sample contained in the well used for the Loading step.
- Loading Conc. (µg/ml): the concentration of the sample in the well used for the Loading step, units in micrograms per milliliter.
- Cycle: the experiment cycle number of the assay, with a cycle representing all the programmed steps of a single assay (typically Baseline, Loading, Association, and Dissociation).
- Conc. (nM): the concentration of the sample in the well used for the Association step, units in nanomolar.
- Response: the maximum measured value during the Association step.
- KD (M): the calculated dissociation constant, with units in molar.
- KD Error: the estimated error of the calculated dissociation constant.
- ka (1/Ms): the calculated association rate constant of a single analyte-ligand binding event based on the curve fit to the data, units in per molar per second.
- ka2: the calculated association rate constant of an analyze-ligand complex binding to a second ligand molecule.
- ka Error: the estimated error of the calculated association rate constant.
- ka2 Error: the estimated error of the calculated association rate constant for a second binding event.
- kdis (1/s): the calculated dissociation rate constant of a single analyte-ligand binding event based on the curve fit to the data, units of per second.
- kdis2: the calculated dissociation rate constant of an analyte-ligand complex bound to a second ligand.
- kdis Error: the estimated error of the calculated dissociation rate constant.
- kdis2 Error: the estimated error of the calculated dissociation rate constant for a second binding event.
- Rmax: the calculated maximum response if the Association step continued to equilibrium.
- Rmax Error: the estimated error of the calculated Rmax value.
- kobs (1/s): the observed rate constant reflecting the overall rate of the combined association and dissociation of the two binding partners.
- Full X^2: chi-squared value of the fitted curve relative to the experimental data.
- Full R^2: R-squared value describing the correlation of the fitted curve to the experimental data.
- Excel notebook containing the full kinetics tables for each antibody-HA experiment.
Folder: ChimeraX_visualization_of_Xtal_maps
Description: Folder containing ChimeraX sessions with visualized models and maps of the TJ2 and J4 crystal structures.
- File: TJ2_map.cxs
- Description: ChimeraX session of the COBRA HA TJ2 with the visualized electron density map.
- File: J4_map.cxs
- Description: ChimeraX session of the COBRA HA J4 with the visualized electron density map.
- File: README.txt
- Description: Text file describing the files and the software version needed to open the files.
The BLI data was collected on an Octet Red384 instrument in the Macromolecular Structure Funtion Core Facility. Data processing was performed using the Octet Data Analysis HT software v7. Molecular models were obtained from the AlphaFold3 server (https://alphafoldserver.com).