REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Monoclonal ANTI-FLAG M2 antibody	Sigma Aldrich	Cat# F1804; RRID: AB_262044
Anti-HA antibody produced in rabbit	Sigma Aldrich	Cat# H6908; RRID: AB_260070
Goat anti-rabbit IgG Dylight488 conjugated	Invitrogen	Cat# 35552; RRID: AB_844398
Goat anti-mouse IgG Dylight633 conjugated	Invitrogen	Cat# 35512; RRID: AB_1307538
Anti-rabbit peroxidase antibody produced in goat	Sigma Aldrich	Cat# A9169; RRID: AB_258434
Anti-mouse IgG Peroxidase antibody produced in goat	Sigma Aldrich	Cat# A4416; RRID: AB_258167
Anti-His antibody produced in mouse	Cell Signaling Technology	Cat# 9991; RRID: AB_2797714
Goat polyclonal anti-RMND5A antibody	Santa Cruz	Cat# sc-161202, RRID: AB_2181510
Sheep polyclonal anti-MAEA antibody	R&D Systems	Cat# AF7288-SP, RRID: AB_10971438
Rabbit polyclonal anti-RANBP9 antibody	Abnova	Cat# PAB16671; RRID: AB_10677213
Rabbit polyclonal anti-TWA1 antibody	Novus	Cat# NBP1-32596; RRID: AB_2274921
Mouse monoclonal anti-ARMC8 antibody	Santa Cruz	Cat# sc-365307; RRID: AB_10850172
Mouse monoclonal anti-MKLN1 antibody	Santa Cruz	Cat# sc-398956; RRID: AB_2737249
Rabbit polyclonal anti-WDR26 antibody	Bethyl Laboratories	Cat# A302-245A; RRID: AB_1730876
Rabbit polyclonal anti-YPEL5 antibody	Thermo Fisher	Cat# PA5-26957; RRID: AB_2544457
Sheep polyclonal anti-hGid4	This study	N/A
HaloLink Resin	Promega	Cat# G1912
ANTI-FLAG M2 affinity gel	Sigma Aldrich	Cat# A2220
His-Select Nickel affinity gel	Sigma Aldrich	Cat# P6611
Glutathione Sepharose 4B	GE Healthcare	Cat# 17075605
StrepTactin Sepharose High Performance resin	cytiva	Cat# 28935599
His-Halo UBAUBQLN1	This study	N/A
Critical commercial assays
EnzChek Phosphate Assay Kit	ThermoFisher Scientific	Cat# E6646
Bacterial and virus strains
E. coli BL21 RIL (DE3)	MPIB	N/A
E. coli DH5α	MPIB	N/A
Chemicals, peptides, and recombinant proteins
complete EDTA free	Roche	Cat# 05056489001
Aprotinin from bovine lung	Sigma	A1153-10MG
Leupeptin	Sigma	L2884-250MG
Benzamidine	Sigma	B6506-25G
GGGGGFYVK-FAM	MPIB	N/A
PTLVNGWPR	MPIB	N/A
PTLVNGPRRDSTEGFTGRGWSGRGWS KGGK-FAM	MPIB	N/A
PGLWRSPRRDSTEGFTGRGWSGRG WSKGGK-FAM	MPIB	N/A
3xFLAG peptide	MPIB	N/A
Deposited data
Apo Chelator-GIDSR4	This study	EMDB: EMD-12541
Chelator-GIDSR4 + Fbp1	This study	EMDB: EMD-12557
GIDSR4	This study	EMDB: EMD-12548
SRS module	This study	EMDB: EMD-12559; PDB: 7NS3
Cat module	This study	EMDB: EMD-12560; PDB: 7NS4
SA module	This study	EMDB: EMD-12563; PDB: 7NSB
Endogenous GIDAnt	This study	EMDB: EMD-12538
Endogenous Chelator-GIDAnt	This study	EMDB: EMD-12540
CTLHSR4	This study	EMDB: EMD-12537
CTLHSR4 SRS module	This study	EMDB: EMD-12564; PDB: 7NSC
CTLH-WDR26 SA and SRS modules	This study	EMDB: EMD-12545
CTLH-WDR26 supramolecular assembly	This study	EMDB: EMD-12542
CTLH-MKLN1 SA and SRS modules	This study	EMDB: EMD-12547
Fbp1 (crystal structure)	This study	PDB: 7NS5
Proteomics data	This study	PXD024462
Raw image data	This study	http://dx.doi.org/10.17632/rfpsg6939c.1
Experimental models: Cell lines
Sf9 Insect cells	Thermo Fisher	Cat# 11496015
High Five Insect cells	Thermo Fisher	Cat# B85502
K562 human cells	ATCC	ATCC#CCL-243; RRID: CVCL_00004
Experimental models: Organisms/strains
Saccharomyces cerevisiae: Strain S288C: BY4741; MATa his3Δ1leu2Δ0 met15Δ0 ura3Δ0	Euroscarf	Cat# Y00000
CRLY12; BY4741, Gid4::KANMX	This study	N/A
CRLY14; BY4741, Gid7::KANMX	This study	N/A
CRLY45; BY4741, Gid8::Gid8-3xFLAG-KANMX	Qiao et. al., 2020	N/A
CRLY131; BY4741, Gid2::3xFLAG-Gid2 (K365A)	Qiao et. al., 2020	N/A
CRLY241; BY4741, Gid7::KANMX, Gid8::Gid8-3xFLAG-HPHNT1	This study	N/A
CRLY267; BY4741, Gid7::Gid7-3xHA-HPHNT1, Gid5::Gid5-3xFLAG-KANMX	This study	N/A
CRLY498; BY4741, Fbp1::Fbp1-3xFLAG-HPHNT1, Pdr5::NATNT2	This study	N/A
CRLY504; BY4741, Fbp1::Fbp1-3xFLAG-HPHNT1, Pdr5::NATNT2, Gid7:KANMX	This study	N/A
Recombinant DNA
pCSJ95	Chen et al., 2017	N/A
pCSJ125	Chen et al., 2017	N/A
VBP6; pRS313-pGPD-Pck1-3xFLAG-CYC-pGPD-DHFR-HA-CYC	This study	N/A
DSJC1; pRS313-pGPD-Fbp1-K32R/K35R-3xFLAG-CYC-pGPD-DHFR-HA-CYC	This study	N/A
DSJC2; pRS313-pGPD-Fbp1-K280R/K281R-3xFLAG-CYC-pGPD-DHFR-HA-CYC	This study	N/A
DSJC3; pRS313-pGPD-Fbp1-K32R/K35R/K280R/K281R-3xFLAG-CYC-pGPD-DHFR-HA-CYC	This study	N/A
pRS415-pTEF-CYC	This study	N/A
pRS415-pTEF-GFP-ScGid4-CYC	This study	N/A
pLIB Gid1	This study	N/A
pLIB Gid2	This study	N/A
pLIB Gid4	This study	N/A
pLIB Gid5	This study	N/A
pLIB Gid7	This study	N/A
pLIB Gid8-TEV-2xStrep	This study	N/A
pLIB Gid8	This study	N/A
pLIB Gid9	This study	N/A
pLIB RANBP9	This study	N/A
pLIB RMND5A	This study	N/A
pLIB hGid4	This study	N/A
pLIB ARMC8	This study	N/A
pLIB 2xStrep-3C-ARMC8	This study	N/A
pLIB MAEA	This study	N/A
pLIB WDR26	This study	N/A
pLIB GST-TEV-WDR26	This study	N/A
pLIB MKLN1	This study	N/A
pLIB YPEL5	This study	N/A
pLIB MAEA Y394A	This study	N/A
pLIB RMND5A R340A	This study	N/A
pLIB RMND5A I338A/L339A	This study	N/A
pLIB GST-TEV-Uba1	This study	N/A
pBIG2 Gid1:Gid8-TEV-2xS:Gid5:Gid4:Gid2:Gid9	This study	N/A
pBIG2 Gid1:Gid8-TEV-2xS:Gid5:Gid2:Gid9	This study	N/A
pBIG2 Gid1:Gid8-TEV-2xS:Gid5:Gid2:Gid9:Gid7	This study	N/A
pBIG2 Gid1:Gid8-TEV-2xS:Gid5:Gid4:Gid2:Gid9:Gid7	This study	N/A
pBIG1 RANBP9:TWA1-TEV-2xS:ARMC8	This study	N/A
pBIG1 RANBP9:TWA1:2xS-3C-ARMC8	This study	N/A
pBIG2 RANBP9:TWA1-TEV-2xS:ARMC8:RMND5A:MAEA	This study	N/A
pBIG2 RANBP9:TWA1-TEV-2xS:ARMC8:RMND5A	This study	N/A
pBIG2 RANBP9:TWA1-TEV-2xS:ARMC8:MAEA	This study	N/A
pGEX GST-TEV-Gid4 (Δ1-116)	This study	N/A
pGEX GST-TEV-Gid7	This study	N/A
pGEX GST-TEV-Gid7 (Δ1-285)	This study	N/A
pGEX GST-TEV-hGid4 (Δ1-99)	This study	N/A
pGEX GST-TEV-hGid4 (R189A)	This study	N/A
pGEX GST-TEV-hGid4 (Y154A)	This study	N/A
pGEX GST-TEV-hGid4 (F174A)	This study	N/A
pGEX GST-TEV-hGid4 (F239A)	This study	N/A
pGEX GST-TEV-hGid4 (C156D)	This study	N/A
pGEX GST-TEV-hGid4 (E298A)	This study	N/A
pGEX GST-TEV-hGid4 (H147D)	This study	N/A
pGEX GST-TEV-hGid4 (Y158A/F174A)	This study	N/A
pGEX GST-TEV-hGid4 (Y158A/F239A)	This study	N/A
pGEX GST-TEV-hGid4 (F174A/F239A)	This study	N/A
pGEX GST-TEV-hGid4 (Y297A/F229A)	This study	N/A
pGEX GST-TEV-hGid4 (Δ297-300)	This study	N/A
pRSF Ubc8-6xHis	This study	N/A
pRSF Fbp1-6xHis	This study	N/A
pRSF Fbp1 (K32R/K35R)-6xHis	This study	N/A
pRSF Fbp1 (K280R/K281R)-6xHis	This study	N/A
pRSF Fbp1 (K32R/K35R/K280R/K281R)-6xHis	This study	N/A
pRSF Fbp1-GGGGS-sortag-6xHis	This study	N/A
pRSF Mdh2-GGGGS-sortag-6xHis	This study	N/A
pRSF Pck1-GGGGS-sortag-6xHis	This study	N/A
pQlink Fbp1-TEV-V5-2xS	This study	N/A
pRSF Ube2H-6xHis	This study	N/A
pGEX GST-3C-Ub	This study	N/A
pGEX GST-3C-Ub K0 (all K > R)	This study	N/A
pGEX GST-3C-Ub K6 (all K > R; R6K)	This study	N/A
pGEX GST-3C-Ub K11 (all K > R; R11K)	This study	N/A
pGEX GST-3C-Ub K27 (all K > R; R27K)	This study	N/A
pGEX GST-3C-Ub K29 (all K > R; R29K)	This study	N/A
pGEX GST-3C-Ub K33 (all K > R; R33K)	This study	N/A
pGEX GST-3C-Ub K48 (all K > R; R48K)	This study	N/A
pGEX GST-3C-Ub K63 (all K > R; R63K)	This study	N/A
pET3b Ub	This study	N/A
pET29 sortase A	Chen et al., 2011b	N/A
Software and algorithms
FOCUS	Biyani et al., 2017	https://focus.c-cina.unibas.ch/documentation.php
SerialEM	Mastronarde, 2003	https://bio3d.colorado.edu/SerialEM/
MOTIONCOR2	Zheng et al., 2017	https://emcore.ucsf.edu/ucsf-software
Gctf	Zhang, 2016	https://www2.mrc-lmb.cam.ac.uk/download/gctf/
Gautomatch	Kai Zhang	https://www2.mrc-lmb.cam.ac.uk/download/gautomatch-053/
Relion3.0/3.1	Fernandez-Leiro and Scheres, 2017; Scheres, 2012; Zivanov et al., 2018	https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
Phyre2	Kelley et al., 2015	http://www.sbg.bio.ic.ac.uk/∼phyre2/html/page.cgi?id=index
SWISS-MODEL	Waterhouse et al., 2018	https://swissmodel.expasy.org
UCSF Chimera	Pettersen et al., 2004	https://www.cgl.ucsf.edu/chimera/
UCSF ChimeraX	Goddard et al., 2018	https://www.rbvi.ucsf.edu/chimerax/
PyMOL v2.1	Schrödinger	https://pymol.org/2/
CCP-EM	Burnley et al., 2017	https://www.ccpem.ac.uk/download.php
Buccaneer	Cowtan, 2006	http://www.ysbl.york.ac.uk/∼cowtan/buccaneer/buccaneer.html
Coot	Emsley and Cowtan, 2004; Emsley et al., 2010	https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
Phenix	Adams et al., 2010; Afonine et al., 2018; DiMaio et al., 2013	https://www.phenix-online.org/
Molprobity	Chen et al., 2010	http://molprobity.biochem.duke.edu/
Image Studio	LI-COR Biosciences	https://www.licor.com/bio/image-studio/
Fiji/ImageJ	Schindelin et al., 2012	https://imagej.net/Welcome
GraphPad Prism version 8.0	GraphPad Software	http://www.graphpad.com:443/
ImageQuant TL Toolbox version 8.2	Cytiva (formerly GE Healthcare)	https://www.cytivalifesciences.com
DeepEMhancer	Sanchez-Garcia et al., 2020	http://www.biorxiv.org
Other
QUANTIFOIL® R1.2/1.3, 100 Holey Carbon Films, Grids: Cu 200 mesh	Quantifoil Micro Tools GmbH	https://www.quantifoil.com
IMEM	Thermo Fisher	Cat# 12440-053