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. Author manuscript; available in PMC: 2022 May 12.
Published in final edited form as: Cell Rep. 2022 Apr 19;39(3):110702. doi: 10.1016/j.celrep.2022.110702

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
α-MYC Sigma Aldrich C3956-100UG; RRID: AB_439680
α-His Sigma Aldrich SAB4301134-100UL
α-Dpm1 Thermo Fisher Scientific A-6429; RRID: AB_2536204
α-YFP Takara 632380; RRID: AB_10013427
α-Pgk1 (Baum et al., 1978) N/A
α-PA Jackson Immunoresearch 323-005-024; RRID: AB_2315781
Atg23 antiserum This study N/A
Ape1 antiserum (Klionsky et al., 1992) N/A
Bacterial and virus strains
Rosetta 2 (DE3) pLysS cells Novagen 71401
Chemicals, peptides, and recombinant proteins
Q5 mutagenesis NEB E0554
NuPAGE 4–12% Bis-Tris gels Invitrogen NP0322BOX
LB broth Fisher Scientific BP1426
IPTG IBI Scientific IB02125
Triton X-100 VWR AAA16046-AE
2-mercaptoethanol Sigma Aldrich M6250
cOmplete Mini EDTA-free protease inhibitor tablets Roche 11836170001
Talon resin Clontech 635504
TCEP VWR 97064-848
Yeast polar lipid extracts Avanti Polar Lipids 190001
1.0-μm Nuclepore Track-Etched membrane VWR 15000-610
0.4-μm Nuclepore Track-Etched membrane Sigma Aldrich WHA10417104
0.1-μm Nuclepore Track-Etched membrane VWR 15000-614
Rhodamine PE Avanti Polar Lipids 810150
Polyvinyl alcohol Sigma Aldrich 814894
Alexa Fluor 488 Invitrogen A10254
DiD Thermo Fisher Scientific D7757
Agar Formedium AGA03
Yeast extract Formedium YEA03
Peptone Formedium PEP03
Yeast nitrogen base Formedium CYN0410
Acrylamide National Diagnostics EC-890
Triton X-100 Sigma Aldrich X100-100ML
CHAPS Anatrace C31625GM
Critical commercial assays
QIAprep Spin Miniprep Kit Qiagen 27104
Deposited data
SAXS data for Atg23 This paper SASBDB: SASDL39
SAXS data for Atg23[LIL] This paper SASBDB: SASDL49
Experimental models: Organisms/strains
SEY6210 (MATα leu2-3,112 ura3-52 his3-Δ200 trp1-Δ901 lys2-801 suc2-Δ9 GAL) (Robinson et al., 1988) N/A
WLY176 (SEY6210 pho13Δ, PHQ8::pho8Δ60) (Noda and Klionsky, 2008) N/A
MKO (SEY6210, atg1Δ, 2Δ, 3Δ, 4Δ, 5Δ, 6Δ, 7Δ, 8Δ, 9Δ, 10Δ, 11Δ, 12Δ, 13Δ, 14Δ, 16Δ, 17Δ, 18Δ, 19Δ, 20Δ, 21Δ, 23Δ, 24Δ, 27Δ, 29Δ, 31Δ::ble) (Cao et al., 2008) N/A
KTY14 (SEY6210 atg23Δ::KAN) (Tucker et al., 2003) N/A
yWH59 (SEY6210, ATG23-mNeonGreen::TRP1) This study N/A
yWH67 (SEY6210, atg23L189A-mNeonGreen::TRP1) This study N/A
yWH68 (SEY6210, atg23I182A L189A-mNeonGreen::TRP1) This study N/A
yWH86 (WLY176, CUP1p-GFP-ATG8::LEU2, atg23Δ::URA3) This study N/A
yWH134 (SEY6210, atg1Δ, 9Δ, 23Δ, ATG9-3xGFP, RFP-APE1) This study N/A
yWH174 (SEY6210, atg1Δ, 9Δ, 23Δ, ATG9-3xGFP, RFP-APE1) This study N/A
Oligonucleotides
Oligonucleotide information This study Table S1
Recombinant DNA
pKL1 (pHis2_6xHis-3C_ScAtg23) This study N/A
pKL2 (pHis2_6xHis-3C_ScAtg23L171A,I182A,L189A) This study N/A
pKL137 (pHis2_6xHis-3C_ScAtg23K66E,R67E) This study N/A
pKL138 (pHis2_6xHis-3C_ ScAtg23K66E,R67E,K296E) This study N/A
pKL138 (pHis2_6xHis-3C_ ScAtg23K66E,R67E,K296E) This study N/A
pKL139 (pHis2_6xHis-3C_ ScAtg23K66E,R67E,R74E,R85E,K296E) This study N/A
pRS314 (Centromeric yeast expression plasmid, TRP1) (Sikorski and Hieter, 1989) N/A
pRS414 (Centromeric yeast expression plasmid, TRP1) (Sikorski and Hieter, 1989) N/A
pRS424 (2-micron yeast expression plasmid, TRP1) (Sikorski and Hieter, 1989) N/A
pRS426 (2-micron yeast expression plasmid, URA3) (Sikorski and Hieter, 1989) N/A
pWH1 (pRS424_pCUP1-6xHis-Atg23) This study N/A
pWH4 (pRS424_pCUP1-6xHis-Atg23L171A,I182A,L189A) This study N/A
pWH11 (pRS426_pCUP1-Atg9-MYC) This study N/A
pWH16(pRS314_pNOP1-Atg23-2xPA) This study N/A
pWH21 (pRS426_pCUP1-Atg23-MYC) This study N/A
pWH25 (pRS426_pCUP1-Atg23L171A,I182A,L189A-MYC) This study N/A
pWH67 (pRS424_pCUP1-PA) This study N/A
pWH69 (pRS414_pATG23-Atg23) This study N/A
pWH70 (pRS314_pNOP1-Atg23L171A,I182A,L189A-2xPA) This study N/A
pWH72 (pRS414_pATG23-Atg23L171A,I182A,L189A) This study N/A
pWH130 (pRS424_pCUP1-6xHis-Atg23R166E,K169E,K176E) This study N/A
pWH131 (pRS424_pCUP1-6xHis-Atg23R190E,K193E,K194E) This study N/A
pWH132 (pRS424_pCUP1-6xHis-Atg23K66E,R67E) This study N/A
pWH134 (pRS424_pCUP1-6xHis-Atg23K66E,R67E,K296E) This study N/A
pWH135 (pRS424_pCUP1-6xHis-Atg23K66E,R67E,R74E,R85E,K296E) This study N/A
Software and algorithms
Fiji (ImageJ2 v 2.3.0) (Schindelin et al., 2012) https://imagej.net/software/fiji/
Image Lab v 5.1 Bio-Rad N/A
Prism v 5.0 or 8.2.1 GraphPad https://www.graphpad.com/
Dynamics v 7.1.8 Wyatt Technology https://www.wyatt.com/products/software/dynamics.html
K2D3 (Louis-Jeune et al., 2012) http://cbdm-01.zdv.uni-mainz.de/%7Eandrade/k2d3/
SEDNTERP 20130813 Beta (Laue et al., 1992) http://bitcwiki.sr.unh.edu/index.php/Main_Page
SEDFIT v 16.1 (Schuck et al., 2002) N/A
Astra v 6.0 Wyatt Technology https://www.wyatt.com/products/software/astra.html
Primus v 3.4 (Konarev et al., 2003) https://www.embl-hamburg.de/biosaxs/software.html
GNOM v 5.0 (Konarev et al., 2003) https://www.embl-hamburg.de/biosaxs/software.html
GASBOR v 2.3 (Svergun et al., 2001) https://www.embl-hamburg.de/biosaxs/software.html
SUPCOMB v 2.3 (Svergun et al., 2001) https://www.embl-hamburg.de/biosaxs/software.html
DAMAVER v 5.0 (Volkov and Svergun, 2003) https://www.embl-hamburg.de/biosaxs/software.html
HADDOCK v 2.4 (van Zundert et al., 2016) https://wenmr.science.uu.nl/haddock2.4/
Excel 2021 Microsoft https://www.microsoft.com/en-us/microsoft-365/excel
R v 4.0.5 R Project https://www.r-project.org/
Python v 3.8 Python Software Foundation https://www.python.org/