|
Antibodies
|
| Rabbit polyclonal anti-Sc-Atg44 |
This study |
N/A |
| Guinea pig polyclonal anti-Sp-Atg44 |
This study |
N/A |
| Rabbit polyclonal anti-Atg33 |
This study |
N/A |
| Rabbit polyclonal anti-RFP |
MBL |
Cat# PM005; RRID: AB_591279 |
| Mouse monoclonal anti-GFP (JL-8) |
Takara Bio |
Cat# 632380; RRID: AB_10013427 |
| Mouse monoclonal anti-FLAG |
Sigma-Aldrich |
Cat# F1804; RRID: AB_262044 |
| Rabbit polyclonal anti-DDDDK |
MBL |
Cat# PM020; RRID: AB_591224 |
| Rabbit monoclonal anti-DYKDDDDK tag |
Cell Signaling Technology |
Cat# 14793; RRID: AB_2572291 |
| Rabbit polyclonal anti-ATPB |
Abcam |
Cat# ab128743; RRID: AB_2810299 |
| Rabbit polyclonal anti-Histone H3 |
Abcam |
Cat# ab1791; RRID: AB_302613 |
| Mouse monoclonal anti-HSPD1/HSP60 |
Proteintech |
Cat# 66041-1-Ig; RRID: AB_11041709 |
| Mouse monoclonal anti-Tim23 |
BD Biosciences |
Cat# 611222; RRID: AB_398754 |
| Rabbit polyclonal anti-Tom20 |
Proteintech |
Cat# 21090-1-AP; RRID: AB_10734583 |
| Rabbit polyclonal anti-CHCHD4 |
Santa Cruz Biotechnology |
Cat# sc-11415; RRID: AB_2207533 |
| AF594 F(ab’)2-goat anti-rabbit IgG (H+L) |
Thermo Fisher Scientific |
Cat# A-11072; RRID: AB_2534116 |
| AF594 F(ab’)2-goat anti-mouse IgG (H+L) |
Thermo Fisher Scientific |
Cat# A-11020; RRID: AB_141974 |
| AF647 goat anti-rabbit IgG (H+L) |
Thermo Fisher Scientific |
Cat# A-21244; RRID: AB_2535812 |
| Mouse monoclonal anti-HA |
Sigma-Aldrich |
Cat# H9658; RRID: AB_260092 |
| Mouse monoclonal anti-Pgk1 |
Thermo Fisher Scientific |
Cat# 459250; RRID: AB_2532235 |
| Chicken polyclonal anti-protein A |
GeneTex |
Cat# GTX77595; RRID: AB_379859 |
| Mouse monoclonal anti-Cox2 |
MitoScience |
Cat# MS419; RRID: AB_1618187 |
| Rabbit polyclonal anti-Ape1 |
Kim et al. (1997)34
|
N/A |
| Rabbit polyclonal anti-Atg32 |
Aoki et al. (2011)6
|
N/A |
| AF488 FluoroNanogold conjugated goat anti-rabbit IgG |
Nanoprobes |
Cat# 7204; RRID: AB_2868458 |
| Goat anti-mouse IgG-HRP |
Merck Millipore |
Cat# AP124P; RRID: AB_90456 |
| Goat anti-rabbit IgG-HRP |
Jackson ImmunoResearch |
Cat# 111-035-003; RRID: AB_2313567 |
|
Bacterial and virus strains
|
|
Escherichia coli C41 (DE3) |
Sigma-Aldrich |
Cat# CMC0017 |
|
Escherichia coli BL21(DE3) |
Sigma-Aldrich |
Cat# CMC0014 |
|
Chemicals, peptides, and recombinant proteins
|
| Zymolyase 100T |
Nacalai tesque |
Cat# 07665-55 |
| Lysing Enzymes from Trichoderma harzianum
|
Sigma-Aldrich |
Cat# L1412 |
| Proteinase K, recombinant, PCR Grade |
Roche |
Cat# 03115836001 |
| MitoTracker Red CMXRos |
Thermo Fisher Scientific |
Cat# M7512 |
| FM 4-64 |
Molecular Probes |
Cat# T3166 |
| Block Ace |
DS Pharma Biomedical |
Cat# UKB80 |
| Amylose resin |
New England Biolabs |
Cat# E8021 |
| Ni-NTA Superflow |
QIAGEN |
Cat# 30410 |
| COSMOGEL GST-Accept |
Nacalai tesque |
Cat# 09277-56 |
| Alexa Fluor 647 C2 Maleimide |
Invitrogen |
Cat# A20347 |
| Alexa Fluor 647 hydrazide |
Invitrogen |
Cat# A20502 |
| 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) |
Avanti Polar Lipids |
Cat# 850457 |
| 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) |
Avanti Polar Lipids |
Cat# 850757 |
| L-α-phosphatidylinositol (PI) |
Avanti Polar Lipids |
Cat# 840042 |
| 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine (POPS) |
Avanti Polar Lipids |
Cat# 840034 |
| 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphate (POPA) |
Avanti Polar Lipids |
Cat# 840857 |
| 1’,3’-bis[1,2-dioleoyl-sn-glycero-3-phospho]-glycerol (CL) |
Avanti Polar Lipids |
Cat# 710335 |
| 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(lissamine rhodamine B sulfonyl) (liss Rhod PE) |
Avanti Polar Lipids |
Cat# 810150 |
| D-galactosyl-β-1,1’ N-nervonoyl-D-erythro-sphingosine (GC) |
Avanti Polar Lipids |
Cat# 860546 |
| Silica beads (50 μm) |
Nanocs |
Cat# Si01-50u-1 |
| BSA tracer |
Aurion |
Cat# 210.033 |
| Tamavidin 2 solution |
FUJIFILM Wako |
Cat# 201-21271 |
|
Critical commercial assays
|
| NEBuilder HiFi DNA Assembly Master Mix |
New England Biolabs |
Cat# E2621 |
| PrimeSTAR Mutagenesis Basal Kit |
Takara Bio |
Cat# R046A |
| IgG Sepharose 6 Fast Flow |
GE Healthcare |
Cat# 17096901 |
| EzWestLumi One |
ATTO |
Cat# WSE-7110 |
| EzWestLumi plus |
ATTO |
Cat# WSE-7120 |
| Clarity Max Western ECL Substrate |
Bio-Rad |
Cat# 1705062 |
| FuGENE HD Transfection Reagent |
Promega |
Cat# E2311 |
| Oriole Fluorescent Gel Stain |
Bio-Rad |
Cat# 1610496 |
|
Deposited data
|
| Crystal structure of Sp-Atg44 |
This study |
PDB: 7YDO |
| Unprocessed images (microscopy, gels, and blots) |
This study |
Mendeley data: http://dx.doi.org/10.17632/92p3bx6nnz.1
|
|
Experimental models: Cell lines
|
| Human: HeLa (WT) |
Yamashita et al. (2016)16
|
N/A |
| Human: HeLa (DNM1L KO) |
Yamashita et al. (2016)16
|
N/A |
|
Experimental models: Organisms/strains
|
|
S. cerevisiae strains, see Table S1
|
This study |
N/A |
|
S. pombe strains, see Table S2
|
This study |
N/A |
|
Software and algorithms
|
| Image Lab |
Bio-Rad |
https://www.bio-rad.com/en-jp/product/image-lab-software
|
| MetaMorph 7 |
Molecular Devices |
https://www.moleculardevices.com/products/cellular-imaging-systems/acquisition-and-analysis-software/metamorph-microscopy
|
| Auto Slice & View (version 5.6.0) |
Thermo Fisher Scientific |
https://www.thermofisher.com/jp/ja/home/electron-microscopy/products/software-em-3d-vis/auto-slice-view-4-software.html
|
| Fiji |
Schindelin et al. (2012)42
|
http://fiji.sc/Fiji
|
| Image J |
National Institutes of Health |
https://imagej.nih.gov/ij
|
| Amira (version 5.4.5) |
Thermo Fisher Scientific |
https://thermofisher.com/amira-avizo
|
| Zen 2.1 SP1 |
Carl Zeiss |
https://www.zeiss.com/microscopy/en/products/software/zeiss-zen.html
|
| Huygens Professional |
Scientific Volume Imaging |
https://svi.nl/Huygens-Professional
|
| Astra |
Wyatt Technology |
https://www.wyatt.com/products/software/astra.html
|
| DigitalMicrograph |
Gatan |
https://www.gatan.com/resources/digitalmicrograph-scripts
|
| XDS Program Package |
Kabsch (2010)48
|
https://xds.mr.mpg.de/
|
| PHENIX |
Adams et al. (2010)49
|
https://phenix-online.org/
|
| COOT |
Emsley et al. (2010)50
|
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
|
| UCSF ChimeraX (version 1.3) |
Pettersen et al. (2021)51
|
https://www.rbvi.ucsf.edu/chimerax
|
| PPM 3.0 |
Lomize et al. (2022)25
|
https://opm.phar.umich.edu/ppm_server3_cgopm
|
| Kodec (version 4.4.7.39) |
Ngo et al. (2015)53
|
https://doi.org/10.7554/eLife.04806.031
|
| Prism 9 (version 9.5.1) |
GraphPad Software |
https://www.graphpad.com/
|
