| Antibodies |
| PerCP/Cy5.5 anti-mouse CD45.1 Antibody |
Biolegend |
Cat#110728; RRID:AB_893348 |
| PE-Cy™7 Hamster Anti-Mouse CD95 |
BD Biosciences |
Cat#557653; RRID:AB_396768 |
| Brillant Violet 785™ anti-mouse CD45.2 |
Biolegend |
Cat#109839; RRID:AB_2562604 |
| Anti-mouse CD38, BV510 |
BD Biosciences |
Cat#740129; RRID:AB_2739886 |
| BV711 Rat Anti-Mouse Ig, λ1, λ2 & λ3 Light Chain |
BD Biosciences |
Cat#744527; RRID:AB_2742301 |
| BUV395 Rat Anti-Mouse Ig, κ light chain |
BD Biosciences |
Cat#742839; RRID:AB_2741090 |
| BV421 Rat Anti-Mouse IgM |
BD Biosciences |
Cat#743323; RRID:AB_2741424 |
| PE/Cy7 anti-mouse IgD Antibody |
Biolegend |
Cat#405720; RRID:AB_2561875 |
| PE anti-mouse CD45.2 Antibody |
Biolegend |
Cat#109808; RRID:AB_313445 |
| Anti-mouse CD38 Alexa700 |
Invitrogen |
Cat#56-0381-82 |
| BV786 Rat Anti-Mouse IgD |
BD Biosciences |
Cat#563618; RRID:AB_2738322 |
| Alexa Fluor® 700 anti-mouse IgD Antibody |
BD Biosciences |
Cat#405730 |
| BV605 Rat anti-mouse CD45R/B220 |
BD Biosciences |
Cat#563708; RRID:AB_2738383 |
| PE anti-mouse CD138 (Syndecan-1) Antibody |
Biolegend |
Cat#142504; RRID:AB_10915989 |
| BV510 Rat Anti-Mouse IgD |
BD Biosciences |
Cat#563110; RRID:AB_2737003 |
| Brilliant Violet 421™ anti-mouse IgD Antibody |
Biolegend |
Cat#405725; RRID:AB_2562743 |
| BV510 Rat Anti-Mouse B220/CD45R Clone RA3-6B2 |
BD Biosciences |
Cat#563103; RRID:AB_2738007 |
| BV421 Rat Anti-Mouse IgG1 |
BD Biosciences |
Cat#562580; RRID:AB_2737664 |
| BUV395 Rat Anti-Mouse IgM |
BD Biosciences |
Cat#743329; RRID:AB_2741430 |
| CD4 Monoclonal Antibody (GK1.5), APC-eFluor 780 |
Invitrogen |
Cat#47-0042-80 |
| CD8a Monoclonal Antibody (53-6.7), APC-eFluor 780 |
Invitrogen |
Cat#47-0081-80 |
| F4/80 Monoclonal Antibody (BM8), APC-eFluor 780 |
Invitrogen |
Cat#47-4801-80 |
| Ly-6G Monoclonal Antibody (1A8-Ly6g), APC-eFluor 780 |
Invitrogen |
Cat#47-5931-80 |
| FITC anti-mouse/human CD45R/B220 Antibody |
Biolegend |
Cat#103206; RRID:AB_312991 |
| APC anti-mouse CD43 Antibody |
Biolegend |
Cat#143208; RRID:AB_11149685 |
| APC/Cy7 anti-mouse CD21/CD35 (CR2/CR1) Antibody |
Biolegend |
Cat#123418; RRID:AB_1953275 |
| BV421 Rat Anti-Mouse CD24 |
BD Biosciences |
Cat#562563; RRID:AB_2737002 |
| Anti-mouse CD249 (BP1) FITC |
Thermo |
Cat#11-5891-82; RRID:AB_465295 |
| Alexa Fluor 700 anti-mouse TCRb chain |
BioLegend |
Cat#109224; RRID:AB_1027654 |
| FITC anti-mouse CD21/CD35 (CR2/CR1) Antibody |
BioLegend |
Cat#123408; RRID:AB_940403 |
| PerCP/Cy5.5 anti-mouse/human CD45R/B220 Antibody |
BioLegend |
Cat#103236; RRID:AB_893354 |
| APC anti-mouse CD23 Antibody |
BioLegend |
Cat#101620; RRID:AB_2563438 |
| PE anti-mouse CD24 Antibody |
BioLegend |
Cat#101808; RRID:AB_312840 |
| Anti Mouse CD4 BV510 |
BioLegend |
Cat#100559; RRID:AB_2562608 |
| BV421 Rat Anti-Mouse IgM |
BD Biosciences |
Cat#743323; RRID:AB_2741424 |
| Alkaline Phosphatase AffiniPure Goat Anti-Mouse IgG, Fcγ Fragment Specific |
Jackson ImmunoResearch |
Cat#115-055-071 |
| Purified Rat Anti-Mouse CD16/CD32 (Mouse BD Fc Block™) |
BD Biosciences |
Cat#553142; RRID:AB_394657 |
| Alexa Fluor® 488 anti-mouse CD45.2 Antibody |
Biolegend |
Cat#109816; RRID:AB_492868 |
| Alexa Fluor® 594 anti-mouse CD3 Antibody |
Biolegend |
Cat#100240; RRID:AB_2563427 |
| TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody |
Biolegend |
Cat#155861; RRID:AB_2800693 |
| TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody |
Biolegend |
Cat#155863; RRID:AB_2800694 |
| TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody |
Biolegend |
Cat#155865; RRID:AB_2800695 |
| TotalSeq™-C0304 anti-mouse Hashtag 4 Antibody |
Biolegend |
Cat#155867; RRID:AB_2800696 |
| TotalSeq™-C0305 anti-mouse Hashtag 5 Antibody |
Biolegend |
Cat#155869; RRID:AB_2800697 |
| TotalSeq™-C0306 anti-mouse Hashtag 6 Antibody |
Biolegend |
Cat#155871; RRID:AB_2819910 |
| TotalSeq™-C0307 anti-mouse Hashtag 7 Antibody |
Biolegend |
Cat#155873; RRID:AB_2819911 |
| TotalSeq™-C0308 anti-mouse Hashtag 8 Antibody |
Biolegend |
Cat#155875; RRID:AB_2819912 |
| TotalSeq™-C0309 anti-mouse Hashtag 9 Antibody |
Biolegend |
Cat#155877; RRID:AB_2819913 |
| TotalSeq™-C0310 anti-mouse Hashtag 10 Antibody |
Biolegend |
Cat#155879; RRID:AB_2819914 |
| 09-1B12-UCA |
Produced in house (Corbett et al. 2019) |
N/A |
| 09-1B12-UCA + N55T |
Produced in house |
N/A |
| 09-1B12 |
Produced in house (Andrews et al. 2017) |
N/A |
| 05-2A09-UCA |
Produced in house |
N/A |
| 05-2A09-UCA + N55T |
Produced in house |
N/A |
| 05-2A09 |
Produced in house (Andrews et al. 2017) |
N/A |
| 21-1A01-UCA |
Produced in house |
N/A |
| 21-1A01-UCA- + N55T |
Produced in house |
N/A |
| 21-1A01 |
Produced in house (Andrews et al. 2017) |
N/A |
| 05-2D04-UCA |
Produced in house |
N/A |
| 05-2D04-UCA + N55T |
Produced in house |
N/A |
| 05-2D04 |
Produced in house (Andrews et al. 2017) |
N/A |
| 27-1D08-UCA |
Produced in house |
N/A |
| 27-1D08-UCA + N55T |
Produced in house |
N/A |
| 27-1D08 |
Produced in house (Andrews et al. 2017) |
N/A |
| O1 |
Produced in house |
N/A |
| O2 |
Produced in house |
N/A |
| VRC01 |
Produced in house |
N/A |
| CR6261 |
Produced in house |
N/A |
| Biological samples |
|
|
| H3N2 X-31 |
BEI Resources |
Cat#NR-3483 |
| Mouse adapted H1N1 A/California/07/2009 (maA/Cal/09) |
Sabra Klein and Andrew Pekosz John Hopkins University (Fink et al. 2018) |
N/A |
| Influenza reporter viruses |
Masaru Kanekiyo, NIH (Creanga et al. 2021) |
N/A |
| Chemicals, peptides, and recombinant proteins |
|
|
| Pan B Cell Isolation Kit II, mouse |
Miltenyi Biotec |
Cat#130-104-443 |
| LIVE/DEAD™ Fixable Blue Dead Cell Stain Kit, for UV excitation |
Thermo Fisher Scientific |
Cat#L34962
|
| CountBright™ Absolute Counting Beads, for flow cytometry |
Thermo Fisher Scientific |
Cat#C36950
|
| SIGMAFAST™ p-Nitrophenyl phosphate Tablets |
Sigma |
Cat#N2770-50SET |
| NP40 |
Millipore |
Cat#492016-100ML |
| UltraComp eBeads™ Compensation Beads |
Thermo Fisher Scientific |
Cat#01-2222-42 |
| H3ssF |
Produced in house (Corbett et al. 2019) |
N/A |
| H7ssF |
Produced in house (Corbett et al. 2019) |
N/A |
| Invitrogen™ Molecular Probes™ DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) |
Thermo Fisher Scientific |
Cat#D1306 |
| Chromium Next GEM Single Cell 5’ Kit v2 |
10x Genomics |
Cat#PN-1000263 |
| Library Construction Kit |
10x Genomics |
Cat#PN-1000190 |
| Chromium Single Cell Mouse BCR Amplification Kit |
10x Genomics |
Cat#PN-1000255 |
| Chromium Next GEM Chip K Single Cell Kit |
10x Genomics |
Cat#PN-1000286 |
| Dual Index Kit TT Set A |
10x Genomics |
Cat#PN-1000215 |
| Dual Index Kit TN Set A |
10x Genomics |
Cat#PN-1000250 |
| Penicillin/streptomycin |
Gibco |
Cat#15140163 |
| Puromycin |
Gibco |
Cat#A1113803 |
| Opti-MEM |
Gibco |
Cat#31985088 |
| Bovine Serum Albumin |
Sigma |
Cat#A9418 |
| TransIT-LT1 |
MirusBio |
Cat#2306 |
| Gibson assembly kit |
NEB |
Cat#E5510S |
| ExpiFectamine™ 293 Transfection Kit |
Thermo Fisher Scientific |
Cat#A14525 |
| Ni Sepharose resin |
GE Healthcare |
N/A |
| A/Perth/16/2009 H3 trimer |
Produced in house (Joyce et al. 2016) |
N/A |
| A/Shanghai/02/2013 H7 trimer |
Produced in house (Joyce et al. 2016) |
N/A |
| A/Michigan/45/2015 H1 trimer |
This paper |
N/A |
| A/California/07/2009 H1 trimer |
Produced in house (Sangesland et al. 2019) |
N/A |
| A/Japan/305/1957 H2 trimer |
This paper |
|
| A/Indonesia/05/2005 H5 trimer |
Produced in house (Whittle et al. 2014) |
N/A |
| A/Perth/16/2009 H3 trimerDstem (KO, 45HA2) |
This paper |
N/A |
| A/Shanghai/02/2013 H7 trimerDstem (KO, 45HA2) |
This paper |
N/A |
| A/Michigan/45/2015 H1 trimerDstem (KO, 45HA2) |
This paper |
N/A |
| A/California/07/2009 H1 trimerDstem (KO, 45HA2) |
This paper |
N/A |
| A/Indonesia/05/2005 H5 trimerDstem (KO, 45HA2) |
This paper |
N/A |
| H3ssF-KO (45HA2) |
This paper |
N/A |
| H7ssF-KO (45HA2) |
This paper |
N/A |
| Sigma Adjuvant System |
Sigma-Aldrich |
Cat#S6322 |
| Protein G Sepharose |
GE Healthcare |
Cat#17061802 |
| KAPA HiFi HotStart ReadyMix |
KAPA Biosystems |
Cat#KK2602 |
| Maxima H Minus Reverse Transcriptase |
Thermo Fisher |
Cat#EP0751 |
| HotStarTaq Plus DNA Polymerase |
QIAGEN |
Cat#203603 |
| Buffer RLT |
QIAGEN |
Cat#79216 |
| BirA Biotin-Protein Ligase Bulk Reaction Kit |
Avidity |
Cat#Bulk BirA |
| Alexa Fluor 647 Protein Labeling Kit |
Thermo Fisher |
Cat#A20173 |
| Alexa Fluor 488 Protein Labeling Kit |
Thermo Fisher |
Cat#A10235 |
| Alexa Fluor 594 Protein Labeling Kit |
Thermo Fisher |
Cat#A10239 |
| Alexa Fluor 546 Protein Labeling Kit |
Thermo Fisher |
Cat#A20183 |
| MiSeq Reagent Kit, V2 500 cycles |
Illumina |
Cat#MS-102-2003 |
| 10% PEG 10k |
Hampton Research |
Cat#HR2-084 |
| Lys-C endoproteinase |
NEB |
Cat#P8109S |
| Protease inhibitor cocktail (PIC) |
Roche |
Cat#11697498001 |
| Deposited data |
| VH1-18 heavy chain (HC) and light chain (LC) sequences (see also Data S1) |
This paper |
GenBank IDs: PP507169 - PP508172
|
| X-ray structure of 09-1B12 bound to A/Perth/14/2009 H3N2 hemagglutinin |
This paper |
PDB ID: 8UWA |
| CryoEM structure of A/Perth/16/2009 H3 in complex with flu HA central stem VH1-18 antibody UCA6 |
This paper |
PDB ID: 8UT3, EMDB ID: EMD-42528 |
| CryoEM structure of A/Michigan/45/2015 H1 in complex with flu HA central stem VH1-18 antibody 09-1B12 |
This paper |
PDB ID: 8UT4, EMDB ID: EMD-42529 |
| CryoEM structure of A/Michigan/45/2015 H1 in complex with flu HA central stem VH1-18 antibody UCA6_N55T |
This paper |
PDB ID: 8UT5, EMDB ID: EMD-42530 |
| CryoEM structure of A/Perth/16/2009 H3 in complex with polyclonal Fab from mice immunized with H3 stem nanoparticles-15 days post immunization |
This paper |
PDB ID: 8UT6, EMDB ID: EMD-42531 |
| CryoEM structure of A/Perth/16/2009 H3 in complex with polyclonal Fab from mice immunized with H3 stem nanoparticles-28 days post immunization |
This paper |
PDB ID: 8UT7, EMDB ID: EMD-42532 |
| CryoEM structure of A/Shanghai/1/2013 H7 in complex with polyclonal Fab from mice immunized with H7 stem nanoparticles-15 days post-immunization |
This paper |
PDB ID: 8UT8, EMDB ID: EMD-42533 |
| CryoEM structure of A/Shanghai/1/2013 H7 in complex with polyclonal Fab from mice immunized with H7 stem nanoparticles-28 days post immunization |
This paper |
PDB ID: 8UT9, EMDB ID: EMD-42534 |
| CryoEM structure of A/Perth/16/2009 H3 |
This paper |
EMDB ID: EMD-42535 |
| CryoEM map of A/Shanghai/1/2013 H7 HA |
This paper |
EMDB ID: EMD-42536 |
| Code used to compute frequencies of the VH1-18 QxxV class in human IgM repertoires |
This paper |
https://www.doi.org/10.5281/zenodo.10800716
|
| Experimental models: Cell lines |
|
|
| Human: FreeStyle 293F |
Thermo Fisher |
Cat#R79007; RRID:CVCL_D603 |
| Human: Expi293F |
Thermo Fisher |
Cat#A14527; RRID:CVCL_D615 |
| Canine: MDCK |
ATCC |
Cat#CCL-34; RRID:CVCL_0422 |
| Human: HEK293F |
Gibco |
Cat#R79007; RRID:CVCL_6642 |
| MDCK-SIAT1-PB1 |
Produced in house (Creanga et al. 2021) |
N/A |
| MDCK-SIAT1-H5 |
Produced in house (Creanga et al. 2021) |
N/A |
| MDCK-SIAT1-H7 |
Produced in house (Creanga et al. 2021) |
N/A |
| Expi293F GnTI−
|
Produced in house |
N/A |
| HEK293T-PB1 |
Produced in house (Creanga et al. 2021) |
N/A |
| Experimental models: Organisms/strains |
|
|
| Mouse: B6.SJL-Ptprcapepcb/BoyJ mice |
The Jackson Laboratory |
JAX: 002014; RRID:IMSR_JAX:002014 |
| Mouse: C57BL/6 |
The Jackson Laboratory |
JAX: 000664; RRID:IMSR_JAX:000664 |
| Mouse: 09-1B12-UCA KI mouse (H09-1B12-UCA/WT, k09-1B12-UCA/WT) |
This paper |
N/A |
| Oligonucleotides |
|
|
| TaqMan probes for genotyping |
TransnetYX |
N/A |
| Cocktails of IgG- and IgK-specific primers and thermocycling conditions described previously |
von Boehmer et al. 2016
|
N/A |
| sgRNA |
Lin et al. 2018; Wang et al. 2021
|
N/A |
| Primers for Single Cell BCR Amplification, see Table S4
|
This paper |
N/A |
| Software and algorithms |
|
|
| Flowjo 10.9.0 |
Treestar |
https://www.flowjo.com/; RRID:SCR_008520 |
| Prism 10.1.0 |
GraphPad |
https://www.graphpad.com/; RRID:SCR_002798 |
| IMGT/V-quest |
Brochet et al. 2008; Giudicelli et al. 2011
|
http://www.imgt.org/IMGTindex/V-QUEST.php; RRID:SCR_010749 |
| Geneious Prime |
Biomatters |
https://www.geneious.com/; RRID:SCR_010519 |
| Cell Ranger |
10x Genomics |
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger; RRID:SCR_017344 |
| WebLogo |
Crooks et al., 2004
|
https://weblogo.berkeley.edu; RRID:SCR_010236 |
| Seurat R package |
Standard R Package |
https://satijalab.org/seurat/; RRID:SCR_016341 |
| R circlize 0.4.15 |
R package |
https://cran.r-project.org/web/packages/circlize/index.html; RRID:SCR_002141
|
| Bash 5.1.16 |
GNU Project shell |
https://www.gnu.org/software/bash/; RRID:SCR_021268 |
| Python 3.10 |
Python Programming Language |
https://www.python.org/: RRID:SCR_008394 |
| R 4.1.2 |
The R project for statistical computing |
https://www.r-project.org/; RRID:SCR_001905 |
| Tidyverse (dplyr 1.1.4, readr 2.1.4, ggplot2 3.4.4) |
Wickham et al. 2019
|
https://www.tidyverse.org/packages/; RRID:SCR_019186 |
| Pandas 2.1.1 |
Pandas development team, 2020
|
https://pandas.pydata.org; RRID:SCR_018214 |
| Pandaseq |
Masella et al. 2012
|
https://github.com/neufeld/pandaseq; RRID:SCR_002705 |
| MigMAP |
Sangesland et al. 2019
|
https://github.com/mikessh/migmap
|
| MEGA11 software |
Tamura et al. 2011, 2021
|
https://www.megasoftware.net; RRID:SCR_023017 |
| UCSF ChimeraX |
Pettersen et al.2021
|
https://www.cgl.ucsf.edu/chimerax/; RRID:SCR_015872 |
| Coot 0.9.8 |
Casanal et al. 2020
|
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/; RRID:SCR_014222 |
| Phenix |
Afonine et al. 2018
|
https://phenix-online.org; RRID:SCR_014224 |
| Rosetta |
Conway et al. 2014
|
https://www.rosettacommons.org/home; RRID:SCR_015701 |
| XDSGUI |
XDS program package |
https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSGUI; RRID:SCR_015652 |
| Protonate3D tool |
Molecular Operating Environment, 2020; Labute, 2009
|
RRID:SCR_014882 |
| Amber Tools20 package |
Case et al. 2020
|
https://ambermd.org/index.php; RRID:SCR_014230 |
| NpT ensemble |
Salomon-Ferrer et al. 2013
|
N/A |
| SHAKE algorithm |
Miyamoto, 1992
|
N/A |
| Berendsen algorithm |
Berendsen, 1984
|
N/A |
| GetContacts software |
This paper |
https://getcontacts.github.io/
|
| Other |
|
|
| Mastercycler PCR machine |
Eppendorf |
N/A |
| ELISA readers |
BioTek |
N/A |
| 5 laser ARIA II |
BD Biosciences |
RRID:SCR_018091 |
| 5 laser LSR Fortessa |
BD Biosciences |
RRID:SCR_019601 |
| Qubit |
Thermo Fisher |
RRID:SCR_018095 |
| MiSeq |
Illumina |
RRID:SCR_016379 |
| Nextseq2000 |
Illumina |
RRID:SCR_023614 |
| Tapestation |
Agilent |
RRID:SCR_019394 |
| 5 Laser Aria SORP |
BD Biosciences |
N/A |
| Superdex 200 10/300 Column |
GE Healthcare |
Cat#17517501 |
| Superose 6 10/300 Column |
GE Healthcare |
Cat#17517201 |
| 96 Well glass bottom plate with high performance #1.5 cover glass |
CellVis |
Cat#P96-1.5P |
| CellDiscoverer7 |
Zeiss |
N/A |
| Tangential flow filtration system |
Cytiva |
N/A |
| ViewDrop II seals |
SPT LabTech |
Cat#4150-05600 |
|
Erythrina cristagalli Gel-ECA-Immobilized Lectin |
EY Laboratories |
N/A |
| AKTA size exclusion chromatography (SEC) |
Cytiva |
RRID:SCR_023461 |
| IgG Elution Buffer |
Pierce |
Cat#21009 |
| Cu grids |
EMS |
Cat#CF300-Cu-UL |
| Vitrobot |
Thermo Fisher |
N/A |
| Glacios-2 cryoEM |
Thermo Fisher |
N/A |
| Beam line 24-ID-E |
Advanced Photon Source |
N/A |
| BLItz System (Octet N1) |
Fortebio |
RRID:SCR_023267 |
| Streptavidin biosensors (SA) |
Sartorious |
Cat#18-5019 |
| Prolab Isopro RMH 3000, 5P75-5P76 mice diet |
LabDiet |
https://www.labdiet.com/product/detail/5p76-prolab-isopro-rmh-3000
|
