Key resources table.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| PE anti-human CD28 antibody | BioLegend | Cat # 302940 RRID: AB_2564147 |
| Anti-human CD28 antibody | Bio X Cell | Cat # BE0291 RRID: AB_2687814 |
| PE anti-human CD80 antibody | BioLegend | Cat # 305208 RRID: AB_314504 |
| Allophycocyanin anti-human CD80 antibody | BioLegend | Cat # 305220 RRID:AB_2076147 |
| Allophycocyanin anti-human CD86 antibody | BioLegend | Cat # 374207 RRID: AB_2721448 |
| CF568 anti-mouse IgG antibody | Biotium | Cat # 20802 RRID: N/A |
| Anti-human CD3ε antibody | BioLegend | Cat # 317326 RRID: AB_11150592 |
| Anti-SNX9 antibody | Proteintech | Cat # 15721-1-AP RRID: AB_2286415 |
| Anti-GAPDH antibody | Proteintech | Cat # 10494-1-AP RRID: AB_2263076 |
| AF647 anti-human CD28 antibody | BioLegend | Cat # 302953 RRID: AB_2721412 |
| Anti-PKCθ antibody | Cell Signaling | Cat # 13643S RRID: AB_2798282 |
| CF568 anti-rabbit IgG antibody | Biotium | Cat # 20801 RRID: N/A |
| Atezolizumab | Bio X Cell | Cat # SIM0009 RRID: AB_2894730 |
| Biotin anti-human CD3ε antibody | BioLegend | Cat # 317320 RRID: AB_10916519 |
| Anti-mouse CD3ε antibody | BioLegend | Cat # 100340 RRID: AB_11149115 |
| Anti-mouse CD28 antibody | BioLegend | Cat # 102116 RRID: AB_11147170 |
| TruStain FcX plus | BioLegend | Cat # 156604 RRID: AB_2783138 |
| Allophycocyanin-Cy7 anti-mouse CD3ε antibody | BioLegend | Cat # 100330 RRID: AB_1877170 |
| FITC anti-mouse CD4 antibody | BioLegend | Cat # 317408 RRID: AB_1877170 |
| FITC anti-mouse CD4 antibody | BioLegend | Cat # 100510 RRID: AB_312713 |
| PerCP-Cy5.5 anti-mouse CD8 antibody | BioLegend | Cat # 100734 RRID: AB_2075238 |
| FITC anti-mouse CD8 antibody | BioLegend | Cat # 140404 RRID: AB_10643587 |
| PE anti-mouse CD80 antibody | BioLegend | Cat # 104707 RRID: AB_313128 |
| BV711 anti-mouse CD80 antibody | BioLegend | Cat # 104743 RRID: AB_2810338 |
| Allophycocyanin anti-mouse CD86 antibody | BioLegend | Cat # 105011 RRID: AB_493343 |
| PE-Cy7 anti-mouse CD28 antibody | BioLegend | Cat # 102126 RRID: AB_2617011 |
| AF700 anti-human CD3ε antibody | BioLegend | Cat # 317339 RRID: AB_2563407 |
| FITC anti-human CD4 antibody | BioLegend | Cat # 317408 RRID: AB_571951 |
| PerCP-Cy5.5 anti-human CD8 antibody | BioLegend | Cat # 301031 RRID: AB_893426 |
| PE-Cy7 anti-human CD28 antibody | BioLegend | Cat # 302926 RRID: AB_10644005 |
| PE anti-human CD86 antibody | BioLegend | Cat # 374206 RRID: AB_2721633 |
| BV711 human IFNγ antibody | BioLegend | Cat # 502539 RRID: AB_11218602 |
| PE antti-mouse PD1 antibody | Biolegend | Cat # 109104 RRID: AB_313421 |
| PE anti-mouse PDL1 antibody | Biolegend | Cat # 124308 RRID: AB_2073556 |
| PE anti-GzmB antibody | BioLegend | Cat # 372207 RRID: AB_2687031 |
| PE-Cy7 anti-mouse Ki67 antibody | BioLegend | Cat # 652425 RRID: AB_2632693 |
| Anti-Bcl-xL antibody | Proteintech | Cat # 10783-1-AP RRID: AB_2064724 |
| AF647 anti-rabbit IgG antibody | BioLegend | Cat # 406414 RRID: AB_2563202 |
| BV785 anti-mouse CD45 antibody | BioLegend | Cat # 103149 RRID: AB_2564590 |
| FITC anti-mouse CD8 antibody | Accurate Chemical | Cat # ACL168F RRID: N/A |
| BV610 anti-mouse CD8 antibody | Bio-Rad | Cat # MCA609SBV610 RRID: N/A |
| PE-Dazzle 594 anti-mouse CD62L antibody | BioLegend | Cat # 104448 RRID: AB_2566162 |
| BV650 anti-mouse CD44 antibody | BioLegend | Cat # 103049 RRID: AB_2562600 |
| BV711 anti-mouse IFNγ antibody | BioLegend | Cat # 505835 RRID: AB_11219588 |
| AF488 anti-mouse TNFα antibody | BioLegend | Cat # 506315 RRID: AB_493329 |
| Anti-mouse CD3ε antibody | Abcam | Cat # ab16669 RRID: AB_443425 |
| Allophycocyanin anti-human CD69 antibody | Biolegend | Cat # 310909 RRID: AB_314844 |
| HRP anti-rabbit IgG antibody | Cell IDX | Cat # 2RH-100 RRID: N/A |
| Biological samples | ||
| Human white blood cells | San Diego Blood Bank | Cat # LRS-WBC’s |
| Bacterial and virus strains | ||
| Escherichia coli BL21 (DE3) | New England Biolabs | Cat # C2527I |
| Chemicals, peptides, and recombinant proteins | ||
| Fetal bovine serum | Omega Scientific | Cat # FB-02 |
| DMEM medium | Corning | Cat # 10017CV |
| RPMI 1640 medium | Corning | Cat # 10041CM |
| Sodium pyruvate | Corning | Cat # 25000CI |
| β-mercaptoethanol | Fisher Scientific | Cat # ICN19024283 |
| Penicillin and Streptomycin | GE Healthcare | Cat # SV30010 |
| Trypsin-EDTA (0.25%) | ThermoFisher Scientific | Cat # 25200114 |
| Trypan blue | Sigma | Cat # T8154 |
| HBSS | ThermoFisher Scientific | Cat # 14025134 |
| PBS | ThermoFisher Scientific | Cart # 10010049 |
| Everspark STORM buffer | Idylle | Cat # Everspark |
| 100 nm Red Fluorescent Nanodiamond | Adámas Nanotechnologies | Cat # NDNV100nmHi2ml |
| Furimazine | Aobious | Cat # AOB36539 |
| Janelia Fluor® 646, Maleimide | Tocris Bioscience | Cat # 6590 |
| Alexa Fluor® 647 Streptavidin | Jackson ImmunoResearch | Cat # 016-600-084 |
| Poly-D-Lysine | Sigma-Aldrich | Cat # P6407 |
| Polyethylenimine | Fisher Scientific | Cat # NC1014320 |
| CLIP-Surface Dy547 | New England Biolabs | Cat # S9233S |
| SNAP-Surface Alexa Fluor 647 | New England Biolabs | Cat # S9136S |
| Paraformaldehyde | Fisher Scientific, | Cat # 50980494 |
| Glutaraldehyde | Electron Microscopy Sciences | Cat # 16020 |
| Sodium cacodylate | Electron Microscopy Sciences | Cat # 12300 |
| Triton X-100 | Fisher BioReagents, | Cat # BP151500 |
| LgBiT-SpyCatcher | This study | N/A |
| SpyCatcher-AVI | This study | N/A |
| AP-SpyCatcher | This study | N/A |
| EX-NbALFA | This study | N/A |
| BirA | X. Xu, et al., 2021 | N/A |
| HisTrap HP column | GE Healthcare | Cat # 17524802 |
| Glutathione Agarose Beads | MCLAB | Cat # GAB-300 |
| Superdex 75 Increase 10/300 GL column | GE Healthcare | Cat # 29148721 |
| Superdex 200 Increase 10/300 GL column | GE Healthcare | Cat # 28990944 |
| Zeba Spin Desalting Columns | ThermoFisher Scientific | Cat # P187769 |
| Bovine serum albumin | ThermoFisher Scientific | Cat # 23209 |
| SEE | Toxin Technology | Cat # ET404 |
| SEB | Toxin Technology | Cat # BT202 |
| ViaFluor 405 SE | Biotium | Cat # 30068 |
| Saponin | MilliporeSigma | Cat # 558255 |
| Abatacept | Ira Mellman (Genentech) | N/A |
| Human IgG1 Fc | Bio X Cell | Cat # BE0096 |
| Rapamycin | Fisher BioReagents | Cat # 501126903 |
| Hemin | Sigma Aldrich | Cat # H9039 |
| DAB | TCI Chemicals | Cat # D0077 |
| 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) | Avanti Polar Lipids | Cat # 850457C |
| 1,2-dioleoyl-sn-glycero-3-[(N-(5-amino-1-carboxypentyl) iminodiacetic acid) succinyl] (nickel salt, DGS-NTA-Ni) | Avanti Polar Lipids | Cat # 790404C |
| 1,2-Dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(biotinyl) (sodium salt, Biotin-DPPE) | Avanti Polar Lipids | Cat#: 870285P |
| 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-5000] ammonium salt (PEG5000-PE) | Avanti Polar Lipids | Cat#: 880230C |
| Streptavidin | ThermoFisher Scientific | Cat # S888 |
| Human ICAM1 | Sino Biological | Cat # 10346-H08H |
| Human IL-2 | PeproTech | Cat # 200-02 |
| Human IL-15 | PeproTech | Cat # 200-15 |
| Mouse IFNγ | Biolegend | Cat # 575302 |
| OVA257–264 | Anaspec | Cat # AS-60193-1 |
| Zombie Violet | BioLegend | Cat # 423113 |
| Zombie Aqua | BioLegend | Cat # 423102 |
| Fibronectin | Corning | Cat # 354008 |
| Mouse ICAM1 | Sino Biological | Cat # 50440-M08H |
| BV421 OVA257–264 H-2Kb tetramer | NIH Tetramer Core Facility | N/A |
| Tyramide-488 Reagent | ThermoFisher Scientific | Cat # B40953 |
| Octadecyl Rhodamine B Chloride | Biotium | Cat # 60033 |
| Brefeldin A | Biolegend | Cat # 420601 |
| Collagenase | Worthington Biochemical | Cat # LS004197 |
| Soybean trypsin inhibitor | Worthington Biochemical | Cat # LS003587 |
| Critical commercial assays | ||
| Human IL-2 ELISA MAX™ | BioLegend | Cat # 431804 |
| Mouse IL-2 ELISA MAX™ | BioLegend | Cat # 431001 |
| Mouse IFNγ ELISA MAX™ | BioLegend | Cat # 430801 |
| PCR Mycoplasma Detection Kit | Applied Biological Materials Inc | Cat # G238 |
| Mouse CD3 T cell isolation kit | BioLegend | Cat # 480031 |
| mouse CD8 naïve T cell isolation kit | BioLegend | Cat # 480044 |
| Experimental models: Cell lines | ||
| HEK 293T cells | Ronald Vale (University of California San Francisco) | RRID: CVCL_0063 |
| Phoenix-ECO cells | Ronald Vale (University of California San Francisco) | RRID: CVCL_H717 |
| Platinum E cells | Li-Fan Lu (University of California San Diego) |
RRID: CVCL_B488 |
| Jurkat E6.1 T cells | Arthur Weiss (University of California San Francisco) | RRID: CVCL_0065 |
| Raji B cells | Ronald Vale | RRID: CVCL_0511 |
| B16F10 | ATCC | Cat # CRL-6475, RRID: CVCL_0159 |
| B16OVA | Ananda Goldrath | N/A |
| See Table S1 for the list of cell lines | This study | N/A |
| Experimental models: Organisms/strains | ||
| C57BL/6-Tg (TcraTcrb) 1100Mjb/J (OT-1) | Jackson Laboratory | RRID: IMSR_JAX:003831 |
| B6.129S4-Cd80tm1Shr Cd86tm2Shr/J (Cd80−/− Cd86−/−) | Jackson Laboratory | RRID: IMSR_JAX:003610 |
| C57BL/6J | Jackson Laboratory | RRID: IMSR_JAX:000664 |
| B6.129S2-Cd28tm1Mak/J (Cd28−/−) | Jackson Laboratory | RRID: IMSR_JAX:002666 |
| Cd28−/− OT-1 | This study | N/A |
| Oligonucleotides | ||
| CD28 sgRNAs: 5’-GCTTGTAGCGTACGACAATG-3’ and 5’-GTCCTTTGTGAAGGGATGCC-3’ |
This study | N/A |
| SNX9 sgRNAs: 5’-AATGAACTGACGGTTAATGA-3’ and 5’-GAAACATCAAAGGAGAACGA-3’ |
Ecker, et al., 2022 | N/A |
| Recombinant DNA | ||
| See Table S2 for the list of recombinant DNAs | This study | N/A |
| Software and algorithms | ||
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| Micro-Manager | Open Imaging, Inc. | https://micro-manager.org/ |
| AccPbFRET | (Roszik et al., 2008) | http://biophys.med.unideb.hu/accpbfret/ |
| GraphPad Prism | GraphPad Software Inc. | https://www.graphpad.com/scientific-software/prism/ |
| FlowJo | FlowJo, LLC | https://www.flowjo.com/ |
| ThunderSTORM | (Ovesný et al., 2014) | https://zitmen.github.io/thunderstorm/ |
| Coloc-Tesseler software | (Levet et al., 2019) | http://www.iins.u-bordeaux.fr/team-sibarita-Coloc-Tesseler |
| PyMOL | Schrödinger, Inc |
https://pymol.org/2/ RRID:SCR_000305 |