KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| 10.04.7.1C01 mAb | Ellebedy laboratory (Ellebedy et al., 2020) | N/A |
| 10.04.28.1F03 mAb | Ellebedy laboratory (Ellebedy et al., 2020) | N/A |
| 10.04.28.1H09 mAb | Ellebedy laboratory (Ellebedy et al., 2020) | N/A |
| 10.43.7.1A06 mAb | Ellebedy laboratory (Ellebedy et al., 2020) | N/A |
| 10.43.7.1B02 mAb | Ellebedy laboratory (Ellebedy et al., 2020) | N/A |
| 10.43.7.1B04 mAb | Ellebedy laboratory (Ellebedy et al., 2020) | N/A |
| 10.43.28.1B02 mAb | Ellebedy laboratory (Ellebedy et al., 2020) | N/A |
| 10.43.28.1A08 mAb | Ellebedy laboratory (Ellebedy et al., 2020) | N/A |
| 10.43.28.1A02 mAb | Ellebedy laboratory (Ellebedy et al., 2020) | N/A |
| 10.43.28.1E01 mAb | Ellebedy laboratory (Ellebedy et al., 2020) | N/A |
| 10.43.28.1H01 mAb | Ellebedy laboratory (Ellebedy et al., 2020) | N/A |
| Peroxidase AffiniPure Goat Anti-Human IgG (H+L) | Jackson ImmunoResearch | Cat #109-035-088 |
| SIGMAFAST OPD | Sigma Aldrich | Cat #P9187 |
|
Bacterial and virus strains | ||
| 6:2 re-assortant, low pathogenic (no multi-basic cleavage site) H5N1 virus (A/Indonesia/05/2005 and PR8 IBCDC-RG (H5N1)) | Rafi Ahmed laboratory (Ellebedy et al., 2020) | N/A |
|
Biological samples | ||
| Serum from human subjects | Rafi Ahmed laboratory (Ellebedy et al., 2020) | NCT01910519 |
|
Chemicals, peptides, and recombinant proteins | ||
| H5N1 monovalent, inactivated vaccine | GlaxoSmithKline | N/A |
| AS03 | GlaxoSmithKline | N/A |
| HA from A/Indonesia/5/2005 (H5N1) | International Reagent Resource | FR-59 |
| Trimeric head domain of HA from A/Indonesia/5/2005 | Rafi Ahmed laboratory (Ellebedy et al., 2014) | N/A |
| Chimeric HA: stem from A/Indonesia/5/2005, head from A/guinea fowl/Hong Kong/WF10/1999 (H9N2) | Rafi Ahmed laboratory (Ellebedy et al., 2014) | N/A |
| HA from A/California/04/2009 (H1N1) | Produced in house | N/A |
| HA from A/Michigan/45/2015 (H1N1) | Ian Wilson laboratory | N/A |
| HA from A/Singapore/1/1957 (H2N2) | Adrian McDermott laboratory | N/A |
| HA from A/Singapore/INFIMH-16-0019/2016 (H3N2) | James Crowe laboratory | N/A |
| Protein G Resin 4 FastFlow | GE Healthcare | Cat #17-0618-05 |
| CaptureSelect IgG-Fc (ms) Affinity Matrix | Thermo Fisher | Cat #1912855250 |
| Immobilized papain | Thermo Fisher | Cat #20341 |
| Papain from papaya latex | Sigma Aldrich | Cat #P3125 |
| Superose 6 increase 10/300 size exclusion column | GE Healthcare | Cat #17-5172-01 |
| Superdex 200 increase 10/300 size exclusion column | GE Healthcare | Cat #17-5175-01 |
| CaptureSelect CH1-XL column | Thermo Fisher | Cat #494346201 |
| Uranyl Formate | Electron Microscopy Sciences | Cat #D310 25 GM |
| Lauryl Maltose Neopentyl Glycol | Anatrace | Cat #NG310 5 GM |
| Zeba Spin Desalting Columns, 7K MWCO | Thermo Fisher | Cat #89883 |
| 20X HBS-EP buffer | Teknova | Cat #H8022 |
| Bovine Serum Albumins | Sigma Aldrich | Cat #A7906 |
|
Critical commercial assays | ||
| EZ-Link-NHS-PEG4-Biotin | Thermo Fisher | Cat # 21363 |
| Streptavidin (SA) Biosensors | ForteBio | Cat #18-5019 |
| CM5 sensor chips | GE Healthcare | Cat #29149604 |
|
Deposited data | ||
| Polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 4 at day 21 | EMDataBank | EMD-22536 |
| Polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 4 at day 28 | EMDataBank | EMD-22537 |
| Polyclonal immune complex of Fab binding the side of the head of H5 HA from serum of subject 4 at day 28 | EMDataBank | EMD-22538 |
| Polyclonal immune complex of Fab binding the side of the head of H5 HA from serum of subject 4 at day 28 | EMDataBank | EMD-22539 |
| Polyclonal immune complex of Fab binding the receptor binding site region of H5 HA from serum of subject 4 at day 28 | EMDataBank | EMD-22540 |
| Polyclonal immune complex of Fab binding the top of the head of H5 HA from serum of subject 4 at day 28 | EMDataBank | EMD-22541 |
| Polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 4 at day 42 | EMDataBank | EMD-22542 |
| Polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 28 at day 7 | EMDataBank | EMD-22543 |
| Polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 28 at day 21 | EMDataBank | EMD-22544 |
| Polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 28 at day 28 | EMDataBank | EMD-22545 |
| Polyclonal immune complex of Fab binding the receptor binding site region of H5 HA from serum of subject 28 at day 28 | EMDataBank | EMD-22546 |
| Polyclonal immune complex of Fab binding the top of the head of H5 HA from serum of subject 28 at day 28 | EMDataBank | EMD-22547 |
| Polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 36 at day 0 | EMDataBank | EMD-22548 |
| Polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 36 at day 7 | EMDataBank | EMD-22549 |
| Polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 36 at day 21 | EMDataBank | EMD-22550 |
| Polyclonal immune complex of Fab binding the receptor binding site region of H5 HA from serum of subject 36 at day 28 | EMDataBank | EMD-22551 |
| Polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 36 at day 500 | EMDataBank | EMD-22552 |
| Polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 43 at day 7 | EMDataBank | EMD-22553 |
| Polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 43 at day 7 | EMDataBank | EMD-22554 |
| Polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 43 at day 21 | EMDataBank | EMD-22555 |
| Polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 43 at day 28 | EMDataBank | EMD-22556 |
| Polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 43 at day 28 | EMDataBank | EMD-22557 |
| Polyclonal immune complex of Fab binding the receptor binding site region of H5 HA from serum of subject 43 at day 28 | EMDataBank | EMD-22558 |
| Polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 43 at day 100 | EMDataBank | EMD-22559 |
| Polyclonal immune complex of Fab binding the receptor binding site region of H5 HA from serum of subject 43 at day 100 | EMDataBank | EMD-22560 |
| Monoclonal immune complex of Fab 1A06 from participant 43 at day 7 binding the stem of H5 HA | EMDataBank | EMD-22561 |
| Monoclonal immune complex of Fab 1B02 from participant 43 at day 7 binding the stem of H5 HA | EMDataBank | EMD-22562 |
| Monoclonal immune complex of Fab 1B04 from participant 43 at day 7 binding the stem of H5 HA | EMDataBank | EMD-22563 |
| Monoclonal immune complex of Fab 1A02 from participant 43 at day 28 binding the stem of H5 HA | EMDataBank | EMD-22564 |
| Monoclonal immune complex of Fab 1A08 from participant 43 at day 28 binding the stem of H5 HA | EMDataBank | EMD-22565 |
| Monoclonal immune complex of Fab 1H01 from participant 43 at day 28 binding the stem of H5 HA | EMDataBank | EMD-22566 |
| Monoclonal immune complex of Fab 1E01 from participant 43 at day 28 binding the stem of H5 HA | EMDataBank | EMD-22567 |
| Polyclonal immune complex of Fab binding the stem of H1 HA from serum of subject 43 at day 21 | EMDataBank | EMD-22568 |
| CryoEM polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 4 at day 28 | EMDataBank | EMD-22569 |
| CryoEM polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 4 at day 28 | EMDataBank | EMD-22570 |
| CryoEM polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 4 at day 28 | EMDataBank | EMD-22571 |
| CryoEM polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 4 at day 28 | EMDataBank | EMD-22572 |
|
Experimental models: cell lines | ||
| Chicken red blood cells | Lampire | Cat #7241408 |
| Freestyle 293-F cells | Thermo Fisher | Cat# R79007 |
|
Software and algorithms | ||
| Unicorn 7.0 | GE Healthcare | https://www.cytivalifesciences.com/ |
| Leginon | Suloway et al. (2005) | N/A |
| Appion | Lander et al. (2009) | N/A |
| DoG Picker | Voss et al. (2009) | N/A |
| Relion | Scheres (2012) | N/A |
| Cryosparc2 | Punjani et al. (2017) | N/A |
| UCSF Chimera | Pettersen et al. (2004) | N/A |
|
Other | ||
| Negative stain EM grids, 400 mesh | Electron Microscopy Sciences | Cat #EMS400-CU |
| CryoEM grids, quantifoil 1.2/1.3, 00 mesh | Electron Microscopy Sciences | Q4100CR1.3-2nm |