KEY RESOURCES TABLE
| REAGENT or RESOURCE |
SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-CUL5 (rabbit) | Bethyl | Cat# A302-173A |
| Anti-CBFß (rabbit) | Santa Cruz Biotechnology | Cat# sc-56751 |
| Anti-ELOB (rabbit) | Abcam | Cat# ab154854 |
| Anti-ARIH2 (rabbit) | Abcam | Cat# EPR7670 |
| Anti-ALIX (mouse) | Biolegend | Cat# 634502 |
| Anti-HA (mouse) | Covance | Cat# 16B12 |
| Anti-p24 (mouse) | NIH AIDS Reagent Program | Cat# 6521 |
| Anti-vif (rabbit) | NIH AIDS Reagent Program | Cat# 809 |
| Anti-HIV-1 Core Antigen Clone KC57 FITC (mouse) | Beckmann Coulter | Cat# 41116015 |
| Anti-GAPDH (mouse) | Sigma-Aldrich | Cat# G8795-100UL |
| Anti-Flag Hrp (mouse) | Sigma-Aldrich | Cat# A8592-1MG |
| Anti-APOBEC3G (mouse) | NIH AIDS Reagent Program | Cat# 10069 |
| Anti-Rabbit Hrp (goat) | Bio-RAD | Cat# 170-6515 |
| Anti-Mouse Hrp (goat) | Bio-RAD | Cat# 172-1011 |
| Anti-Goat Hrp (rabbit) | Bio-RAD | Cat# 172-1034 |
| Anti-c-myc | Sigma-Aldrich | Cat# M4439 |
| Anti-CD3 (UCHT1) | Tonbo Biosciences | Cat# 70-0038 |
| Anti-CD28 (CD28.2) | Tonbo Biosciences | Cat# 70-0289 |
| Bacterial and Virus Strains | ||
| HIV-1 NL4-3 ΔEnv | This study | N/A |
| HIV-1 NL4-3 ΔEnv ΔVif | This study | N/A |
| HIV-1 NL4-3 | Mulder et al., 2010 | N/A |
| HIV-1 NL4-3 ΔVif | Stanley et al., 2012 | N/A |
| HIV-1 NL4-3 Nef-IRES Gfp | Schindler et al., 2003; NIH AIDS Reagent Program | Cat# 11349 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Anti-FLAG® M2 Magnetic Beads | Sigma | Cat# M8823 |
| 3xFlag peptide | ELIM Biopharm | Custom order |
| RapiGest SF Surfactant | Waters | Cat# 186001861 |
| Sequencing grade trypsin | Promega | Cat# V5113 |
| MG132 | Calbiochem | Cat# 474790 |
| PolyJet transfection reagent | SigmaGen Laboratories | Cat# SL100688 |
| TransIT-293 Transfection Reagent | Mirus | Cat# MIR2700 |
| PhosStop™ phosphatase inhibitors | Roche | Cat# 04906837001 |
| cOmplete™ Protease Inhibitor Cocktail | Roche | Cat# 11836153001 |
| Cas9 protein | QB3 Macrolab, University of California, Berkeley | Custom order |
| Blasticidin | Gibco | Cat# R210-01 |
| Zeocin | Invitrogen | Cat# R250-01 |
| Doxycycline | Clontech | Cat# 631311 |
| Human IL-2 IS | Miltenyi Biotec | Cat# 130-097-745 |
| Puromycin | Sigma-Aldrich | Cat# P8833 |
| 1,10-Phenanthroline | Sigma-Aldrich | Cat# 131377 |
| Polybrene (Hexadimethrine bromide) | Sigma-Aldrich | Cat# H9268 |
| Polyethylenimine (PEI) | Polysciences | Cat# 23966-1 |
| Deposited Data | ||
| Shotgun proteomics RAW and analyzed data | This study | https://www.ebi.ac.uk/pride/archive/projects/PXD009012 |
| Targeted proteomics RAW and analyzed data | This study | https://panoramaweb.org/project/UCSF%20-%20Krogan%20Lab/CRL5_HIV_interactome/begin.view? |
| Experimental Models: Cell Lines | ||
| T-REx Jurkat Cell Line | Jager et al., 2011a | N/A |
| 293T (ATCC CRL-3216) | ATCC | Cat# CRL-3216 |
| CUL5-2xStrep-3xFlag T-REx Jurkat Cell Line | This study | N/A |
| CBFß-2xStrep-3xFlag T-REx Jurkat Cell Line | This study | N/A |
| ELOV-2xStrep-3xFlag T-REx Jurkat Cell Line | This study | N/A |
| 293T ARIH2 KO cell line clone #1 | This study | N/A |
| 293T ARIH2 KO cell line clone #2 | This study | N/A |
| CEM Gfp cells | NIH AIDS Reagent Program, (Gervaix et al., 1997) | Cat# 3655 |
| Oligonucleotides | ||
| See Table S4 for all oligonucleotides | ||
| Recombinant DNA | ||
| pcDNA4: CUL5 | This study | N/A |
| pcDNA4: CBFß | This study | N/A |
| pcDNA4: ELOB | This study | N/A |
| CRISPR lenti: ARIH2 guide 1 | This study | N/A |
| CRISPR lenti: ARIH2 guide 2 | This study | N/A |
| pGEX-TEV-UBE2L3 (UBCH7) | Duda et al., 2013 | N/A |
| pGEX-TEV-ARIH2 | Kelsall et al., 2013 | N/A |
| pGEX2TK UB (C) | Scott et al., 2014 | N/A |
| pGEX NEDD8 | Walden et al., 2003a | N/A |
| pGEX APPBP1-UBA3 | Walden et al., 2003b | N/A |
| pGEX UBE2F | Huang et al., 2009 | N/A |
| pFastbac CUL5 | This study | N/A |
| pFastbac RBX2 | This study | N/A |
| pACYC Elongin C (17-112)-Elongin B (1-118) | This study | N/A |
| pET3a ASB9-TEV-His6 | This study | N/A |
| pGEX6p1 GST-3C-ARIH2 | This study | N/A |
| pGEX GST-TEV-ARIH1 | Duda et al., 2013 | N/A |
| pRSF Duet His6-GB1-TEV-CRL5/RBX2 | Jager et al., 2011b | N/A |
| pCDF Duet-1 Elongin B (1-118) Elongin C (17-112) | Jager et al., 2011b | N/A |
| pET Duet NL43 Vif/CBF-beta | Binning et al., 2018 | N/A |
| pET28b His6-thrombin-Sumo-Uba1 | Olsen and Lima 2013 | N/A |
| pHIS His6-TEV-UBE2R1 | Jager et al., 2011b | N/A |
| pGEX6p1 GST-3C-UBE2L3 | This study | N/A |
| pGEX27a His6-Ubiquitin | Binning et al., 2018 | N/A |
| pGEX-2TK GST-thrombin-PKA-NEDD8 | Huang et al., 2005 | N/A |
| pFastbac APOBEC3G-myc-TEV-GFPII | Binning et al., 2018 | N/A |
| pGEX-4T3 pGSTHsAPPBP1rbsUBA3 | Huang et al., 2005 | N/A |
| pHIS-TEV-UBE2F | Stanley et al., 2012 | N/A |
| Software and Algorithms | ||
| MaxQuant | Cox J et al., 2008 | http://www.coxdocs.org/doku.php?id=:maxquant:start |
| MSstats | M. Choi et al., 2014 | http://msstats.org |
| SAINTexpress | H. Choi et al., 2011 | http://saint-apms.sourceforge.net/ |
| Skyline | MacLean et al., 2010 | https://skyline.ms/project/home/software/Skyline/begin.view |
| Prism 6 | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| Cytoscape | Shannon et al., 2003 | http://www.cytoscape.org/ |
| FlowJo | FlowJo | https://www.flowjo.com/ |
| Other | ||
| Orbitrap Fusion Tribrid Mass Spectrometer | Thermo Fisher Scientific | Cat#IQLAAEGAAPFADBMBCX |
| TSQ Quantiva Triple Quadrupole Mass Spectrometer | Thermo Fisher Scientific | Cat#IQLAAEGAAXFAOUMZZZ |
| EASY-nLC 1200 System | Thermo Fisher Scientific | Cat#LC140 |