Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Cell line (Homo sapiens) | HeLa human epithelial cell line | ATCC | CCL-2 | Authenticated by STR profiling; tested negative for mycoplasma |
| Cell line (Homo sapiens) | WIPI2-KO cells: HeLa cell line gene-edited to knockout WIPI2 expression | Fischer et al., 2020 | ||
| Recombinant DNA reagent | pHTC HaloTag | Promega | G7711 | |
| Recombinant DNA reagent | Halo-WIPI2-WT (Homo sapiens) plasmid for transfection | Stavoe et al., 2019 | Addgene 175025 | Available from Addgene |
| Recombinant DNA reagent | Halo-WIPI2-H85E (Homo sapiens) plasmid for transfection | Modified from Halo-WIPI2-WT in Stavoe et al., 2019 | Addgene 175027 | Available from Addgene |
| Recombinant DNA reagent | Halo-WIPI2-K88E (Homo sapiens) plasmid for transfection | Modified from Halo-WIPI2-WT in Stavoe et al., 2019 | Addgene 175028 | Available from Addgene |
| Recombinant DNA reagent | Halo-WIPI2-I92E(Homo sapiens) plasmid for transfection | Modified from Halo-WIPI2-WT in Stavoe et al., 2019 | Addgene 175029 | Available from Addgene |
| Recombinant DNA reagent | Halo-WIPI2-R108E (Homo sapiens) plasmid for transfection | Stavoe et al., 2019 | Addgene 176004 | Available from Addgene |
| Recombinant DNA reagent | Halo-WIPI2-H85/K88/I92E (Homo sapiens) plasmid for transfection | Modified from Halo-WIPI2-WT in Stavoe et al., 2019 | Addgene 175033 | Available from Addgene |
| Antibody | Anti-LC3B, (Rabbit polyclonal) primary antibody | Abcam | Cat.#ab48394 | IF (1:1000) |
| Antibody | Anti-Rabbit AlexaFluor488, (Goat polyclonal) secondary antibody | ThermoFisher | Cat.#A11034 | IF (1:1000) |
| Chemical compound, drug | TMRDirect Halo Ligand | Promega | Cat.#G2991 | 37.5 nM final concentration |
| Software, algorithm | FIJI | PMID:22743772 | ||
| Software, algorithm | Ilastik | PMID:31570887 | ||
| Software, algorithm | Adobe Illustrator 2021 | Adobe | ||
| Software, algorithm | Prism 9 | GraphPad | ||
| Other | 35 mm #1.5 glass bottom imaging dishes | MatTek | Cat.# P35G-1.5–20 C | |
| Other | EBSS | ThermoFisher | Cat.# 24010043 | |
| Cell line (Homo sapiens) | HEK GnTi | ATCC | CRL-3022 | |
| Recombinant DNA reagent | pCAG-WIPI2d-cs-TEV | Fracchiolla et al., 2020 | Addgene 171419 | |
| Recombinant DNA reagent | pCAG-WIPI2d10-364Δ263–295-cs-TEV | This paper | Addgene 171830 | Materials and methods section: Plasmids |
| Recombinant DNA reagent | pCAG-WIPI2dH85E-cs-TEV | This paper | Addgene 171831 | Materials and methods section: Plasmids |
| Recombinant DNA reagent | pCAG-WIPI2dK88E-cs-TEV | This paper | Addgene 171832 | Materials and methods section: Plasmids |
| Recombinant DNA reagent | pCAG-WIPI2dI92E-cs-TEV | This paper | Addgene 171833 | Materials and methods section: Plasmids |
| Recombinant DNA reagent | pCAG-WIPI2dC93E-cs-TEV | This paper | Addgene 171834 | Materials and methods section: Plasmids |
| Recombinant DNA reagent | pCAG-WIPI2dR108E-cs-TEV | This paper | Addgene 171835 | Materials and methods section: Plasmids |
| Recombinant DNA reagent | pCAG-WIPI2dR125E-cs-TEV | This paper | Addgene 171836 | Materials and methods section: Plasmids |
| Recombinant DNA reagent | pCAG-WIPI2dK128E-cs-TEV | This paper | Addgene 171837 | Materials and methods section: Plasmids |
| Recombinant DNA reagent | pCAG-mcherry-WIPI2d-cs-TEV | Fracchiolla et al., 2020 | Addgene 178912 | |
| Recombinant DNA reagent | pCAG-mcherry-WIPI2dH85E-cs-TEV | This paper | Addgene 171838 | Materials and methods section: Plasmids |
| Recombinant DNA reagent | pCAG-mcherry-WIPI2dK88E-cs-TEV | This paper | Addgene 171839 | Materials and methods section: Plasmids |
| Recombinant DNA reagent | pCAG-mcherry-WIPI2dI92E-cs-TEV | This paper | Addgene 171840 | Materials and methods section: Plasmids |
| Recombinant DNA reagent | pCAG-mcherry-WIPI2dC93E-cs-TEV | This paper | Addgene 171841 | Materials and methods section: Plasmids |
| Recombinant DNA reagent | pCAG-mcherry-WIPI2dR108E-cs-TEV | This paper | Addgene 171842 | Materials and methods section: Plasmids |
| Recombinant DNA reagent | pCAG-mcherry-WIPI2dR125E-cs-TEV | This paper | Addgene 171843 | Materials and methods section: Plasmids |
| Recombinant DNA reagent | pCAG-mcherry-WIPI2dK128E-cs-TEV | This paper | Addgene 171844 | Materials and methods section: Plasmids |
| Recombinant DNA reagent | pLEXm-GST-TEV-ATG14 | Addgene 99329 | ||
| Recombinant DNA reagent | pCAG-TSF-TEV-BECN1 | Addgene 99328 | ||
| Recombinant DNA reagent | pCAG-TSF-TEV-VPS34 | Addgene 99327 | ||
| Recombinant DNA reagent | pCAG-VPS15 |
Stjepanovic et al., 2017
|
Addgene 99326 | |
| Recombinant DNA reagent | pGBdest-ATG12-10xHis-TEV-ATG5-10xHis-TEVcs-ATG16L1-GFP-TEVcs-StrepII, ATG7, ATG10 | Fracchiolla et al., 2020 | Addgene 169077 | |
| Recombinant DNA reagent | pFast BacHT(B)–6xHis-TEV-ATG7 | Fracchiolla et al., 2020 | ||
| Recombinant DNA reagent | pET Duet-1-6xHis-TEV-ATG3 | Fracchiolla et al., 2020 | Addgene 169079 | |
| Recombinant DNA reagent | pET Duet-1-6xHis-TEV-mCherry-LC3B-Gly(∆5 C) |
Zaffagnini et al., 2018
|
Addgene 169168 | |
| Other | 96–2 well,INTELLI-PLATE (original) tray | Molecular Dimensions, Maumee, OH | ||
| Other | Greiner pre-greased 24 well Combo Plate (SBS format) with lid | Molecular Dimensions, Maumee, OH | ||
| Software, algorithm | Nikon Elements microscope imaging software 4.60 | Nikon Corporation, Tokyo, Japan | https://www.nikoninstruments.com/Products/Software/NIS-Elements-Advanced-Research/NIS-Elements-Viewer | |
| Other | Glutathione Sepharose 4B GST-tagged protein purification resin | GE healthcare, Chicago, IL | Cat# 17075605 | |
| Other | Strep-Tactin Superflow high capacity 50 % suspension | IBA Lifesciences,Göttingen, Germany | Cat# 2-1208-010 | |
| Software, algorithm | phenix.refine | PMID:20124702, 22505256, 31588918 |
RRID:SCR_016736 | |
| Software, algorithm | XDS | PMID:20124692 | RRID:SCR_015652 | |
| Software, algorithm | POINTLESS | PMID:21460446 | RRID:SCR_014218 | |
| Software, algorithm | PHASER | PMID:19461840 | RRID:SCR_014219 | |
| Software, algorithm | PyMol | PyMol (pymol.org) | RRID:SCR_000305 | |
| Software, algorithm | APBS | PMID:11517324 | RRID:SCR_008387 | |
| Software, algorithm | SWISS-MODEL | PMID:29788355 | RRID:SCR_018123 | |
| Software, algorithm | Coot | PMID:20383002 | RRID:SCR_014222 | |