KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| 2406a | This paper |
MT551685, MT551729 |
| 2408a | This paper |
MT551686, MT551730 |
| 2408b | This paper |
MT551687, MT551731 |
| 2408c | This paper |
MT551688, MT551732 |
| 2408c.2 | This paper |
MT551689, MT551733 |
| 2408c.3 | This paper |
MT551690, MT551734 |
| 2408c.4 | This paper |
MT551692, MT551735 |
| 2408d | This paper |
MT551691, MT551736 |
| 2408e | This paper |
MT551693, MT551737 |
| 2408e.2 | This paper |
MT551694, MT551738 |
| 2408f | This paper |
MT551695, MT551739 |
| 2411a | This paper |
MT551696, MT551740 |
| 2411a.2 | This paper |
MT551697, MT551741 |
| 2411b | This paper |
MT551698, MT551742 |
| 2411b.2 | This paper |
MT551699, MT551743 |
| 2413a | This paper |
MT551700, MT551744 |
| 2413b | This paper |
MT551701, MT551745 |
| 2413c | This paper |
MT551702, MT551746 |
| 2413d | This paper |
MT551703, MT551747 |
| KIIM | This paper |
MT551684, MT551728 |
| 1538-79 | Tian et al., 2016 |
KX462817, KX462842 |
| 2405p1-12 | This paper |
MT551667, MT551711 |
| 2405p1-72 | This paper |
MT551668, MT551712 |
| 2405p1-80 | This paper |
MT551669, MT551713 |
| 2404-36 | This paper |
MT551665, MT551709 |
| 2404-18 | This paper |
MT551663, MT551707 |
| 2404-20 | This paper |
MT551664, MT551708 |
| 2403-93 | This paper |
MT551662, MT551706 |
| 2403-59 | This paper |
MT551661, MT551705 |
| 2403-16 | This paper |
MT551660, MT551704 |
| 2410-05 | This paper |
MT551670, MT551714 |
| 2410-07 | This paper |
MT551672, MT551716 |
| 2410-78 | This paper |
MT551676, MT551720 |
| 2410-19 | This paper |
MT551673, MT551717 |
| 2410-06 | This paper |
MT551671, MT551715 |
| 2410-68 | This paper |
MT551675, MT551719 |
| 2410-42 | This paper |
MT551674, MT551718 |
| 2410-93 | This paper |
MT551677, MT551721 |
| 2414-27 | This paper |
MT551681, MT551725 |
| 2414-44 | This paper |
MT551682, MT551726 |
| 2414-61 | This paper |
MT551683, MT551727 |
| 2404-E12 | This paper |
MT551666, MT551710 |
| 2410A-A4 | This paper |
MT551678, MT551722 |
| 2410A-A5 | This paper |
MT551679, MT551723 |
| 2410B-G6 | This paper |
MT551680, MT551724 |
| VRC01 | Wu et al., 2010 | RRID: AB_2491019 |
| anti-mouse CD3 Cy5.5PerCP | BD Pharmingen | Cat# 551163; RRID: AB_394082 |
| anti-mouse CD4 Cy5.5PerCP | BioLegend | Cat# 100540; RRID: AB_893326 |
| anti-mouse CD8 Cy5.5PerCP | BD Pharmingen | Cat# 551162; RRID: AB_394081 |
| anti-mouse F4/80 Cy5.5PerCP | BioLegend | Cat# 123128; RRID: AB_893484 |
| anti-mouse B220 TrPE | BD Pharmingen | Cat# 551489; RRID: AB_394219 |
| anti-mouse IgD BV711 | BioLegend | Cat# 405731; RRID: AB_2563342 |
| anti-mouse IgM Cy7PE | eBioscience | Cat# 25-5790-82; RRID: AB_469655 |
| anti-mouse IgG1 FITC | BD Pharmingen | Cat# 553443; RRID: AB_394862 |
| anti-mouse IgG2a FITC | BD Pharmingen | Cat# 553390; RRID: AB_394828 |
| anti-mouse IgG2b FITC | BD Pharmingen | Cat# 553395; RRID: AB_394833 |
| anti-mouse IgG3 FITC | BD Pharmingen | Cat# 553403; RRID: AB_394840 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| C13.G3-AviHis | Tian et al., 2016 | KX462845 |
| ΔC13-AviHis | Tian et al., 2016 | N/A |
| C13.G4-Ferritin | This paper | N/A |
| 426c-degly3 core-Ferritin | Tian et al., 2016 | KX462844 |
| 426c-degly3 core-AviHis | Tian et al., 2016 | KX518319 |
| Δ426c-degly3 core-AviHis | Tian et al., 2016 | KX518320 |
| 426c-degly2 core monomer | Tian et al., 2016 | KX518321 |
| 426c-degly1 core monomer | Tian et al., 2016 | KX518322 |
| 426c-WT.core monomer | Tian et al., 2016 | KX518323 |
| 426c-WT.DS.SOSIP | Tian et al., 2016 | KX462847 |
| eOD-GT8 60mer | Tian et al., 2016 | KX527857 |
| eOD-GT8-AviHis | Tian et al., 2016 | KX527855 |
| ΔeOD-GT8-AviHis | Tian et al., 2016 | KX527856 |
| eOD-GT6 60mer | Tian et al., 2016 | KX527854 |
| eOD-GT6-AviHis | Tian et al., 2016 | KX527852 |
| ΔeOD-GT6-AviHis | Tian et al., 2016 | KX527853 |
| BG505.SOSIP.T332N | Tian et al., 2016 | N/A |
| BG505.DS.SOSIP | (Kwon et al., 2015) | N/A |
| BG505.DS.SOSIP.S241N | This paper | N/A |
| RSC3 | NIH AIDS Reagent Program; Wu et al., 2010 | Cat# 12042 |
| ZM106.DS.SOSIP | Joyce et al, 2017 | N/A |
| CH505.DS.SOSIP | (Cheng et al., 2019) | N/A |
| UG037.8 core | This paper | N/A |
| Poly I:C | Invivogen | Cat# tlrl-pic-5 |
| d45-01dG5 gp120 core | Wu et al., 2015 | PDB: 4XVS_G |
| SuperScript® II Reverse Transcriptase | ThermoFisher Scientific Inc. | Cat# 18064014 |
| SuperScript® III Reverse Transcriptase | ThermoFisher Scientific Inc. | Cat# 18080044 |
| HotStarTaq Plus DNA Polymerase | Qiagen | Cat# 203607 |
| Galanthus nivalis (GNA)-lectin gel | EY Laboratories, Inc. | Cat# A-7401-2 |
| Ni Sepharose™ excel | GE Healthcare | Cat# 17-3712-03 |
| Protein G Sepharose™ 4 Fast Flow | GE Healthcare | Cat# 17-0618-05 |
| SureBlue™ TMB Microwell Peroxidase Substrate | Kirkegaard & Perry Laboratories, Inc. | Cat# 52-00-00 |
| Extravidin-PE | Sigma | Cat# E4011 |
| Streptavidin-APC | ThermoFisher Scientific Inc. | Cat# SA1005 |
| ViViD (LIVE/DEAD® fixable violet dead cell stain) | ThermoFisher Scientific Inc. | Cat# L34964 |
| Critical Commercial Assays | ||
| Bio-Layer Interferometry Antigenicity Analysis | ForteBio | Octet® HTX System |
| MiSeq Reagent Nano kit, ver2 | Illumina, Inc. | Cat# MS-102-2003 |
| Ovation Ultralow System V2 1-96 kit | NuGen Technologies, Inc. | Cat# 0344NB-08 |
| Deposited Data | ||
| Structure of 2411a in complex with glycosylated HIV-1 gp120 core | This paper | PDB: 7JKS |
| Structure of 2413a in complex with deglycosylated HIV-1 gp120 core | This paper | PDB: 7JKT |
| Deep sequencing of B cell repertoire | This paper | PRJNA623583 |
| Experimental Models: Cell Lines | ||
| Mouse: ES clone for VH1-2/LC mouse model | Tian et al., 2016 | N/A |
| Human: Expi293F™ cells | ThermoFisher Scientific Inc. | Cat# A14528; RRID: CVCL_D615 |
| Human: FreeStyle™ 293F cells | ThermoFisher Scientific Inc. | Cat# R79007 |
| Experimental Models: Organisms/Strains | ||
| Mus musculus: VH1-2/LC mouse model; mixed 129/Sv and C57BL/6 strains | Tian et al., 2016 | N/A |
| Recombinant DNA | ||
| VRC2742: mouse IgG2a heavy chain expression vector | This paper | N/A |
| VRC3353: mouse Kappa chain expression vector | This paper | N/A |
| Sequence-Based Reagents | ||
| Primers for single cell RT-PCR in the VH1-2/LC mouse models | Tian et al., 2016 | Table S6 |
| VH1-2 NGS 5’ primer: xj-VH1-1st ACAGGAGCCCACTCCCAGGTGCAG |
Tian et al., 2016 | Table S6 |
| VH1-2 NGS 3’ primer: 3’musCg-2nd CCAGGGGCCAGTGGATAGACHGATGG |
Tian et al., 2016 | Table S6 |
| VK3-20 NGS 5’ primer: 5’ hVK3-20.6 CGCAGCTTCTCTTCCTCCTG |
Tian et al., 2016 | Table S6 |
| VK3-20 NGS 3’ primer: 3’musCk-1st ACTGGATGGTGGGAAGATGGA |
Tian et al., 2016 | Table S6 |
| Software and Algorithms | ||
| GraphPad Prism 8.01 Software | GraphPad Prism Software, Inc. | RRID: SCR_002798 |
| IMGT/V-Quest | (Brochet et al., 2008; Giudicelli et al., 2011) | http://www.imgt.org/IMGT_vquest/vquest; RRID: SCR_010749 |
| WebLogo | (Crooks et al., 2004) | http://weblogo.berkeley.edu/logo.cgi; RRID: SCR_010236 |
| mGSSP | (Sheng et al., 2017) | https://github.com/scharch/SONAR |
| SONAR | (Schramm et al., 2016) | https://github.com/scharch/SONAR |
| CLUSTALO | (Sievers and Higgins, 2018) | http://clustal.org/omega/; RRID: SCR_001591 |
| HKL2000 | HKL Research, Inc. | https://hkl-xray.com/; |
| The PyMol Molecular Graphics System, v1.8.6 | Schrödinger, LLC | https://pymol.org/2/; RRID: SCR_000305 |
| Phenix | (Adams et al., 2004) | https://sbgrid.org/software/; RRID: SCR_014224 |
| FlowJo v.9.9.1 and v.10.6.2 | FlowJo | https://www.flowjo.com; RRID: SCR_008520 |
| R v3.5.2 | The Comprehensive R Archive Network | https://cran.r-project.org/ |