open source gamma spectrometry analysis software Search Results


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Figure 3. Mass Spectrometry of Cellular Proteins Co-precipitated with UbVs (A and B) Mass spectrometry peak intensity ratios are shown (y axis) for immunoprecipitated UbVs (x axis) and co-immunoprecipitated USP15 (A) or USP4 (B). (C) Heatmap representation of the signal intensities for co-precipitated proteins which satisfied the criteria of exhibiting a fold change >10 compared with negative control and not being a contaminant that interacted with anti-FLAG antibody (Mellacheruvu et al., 2013). The signal is calculated as the intensity ratio between the interactor and the product of the UbV bait and USP15, and the interactors are ranked based on average intensities across experiments. Known USP15 physical interactors based on Pathway Commons (Cerami et al., 2011) are shown in black and ubiquitin-related enzymes in red, and the full list of interactors can be found in Table S2.
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resource source identifier antibodies anti bcat2 abclonal  (ABclonal Biotechnology)
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Figure 3. Mass Spectrometry of Cellular Proteins Co-precipitated with UbVs (A and B) Mass spectrometry peak intensity ratios are shown (y axis) for immunoprecipitated UbVs (x axis) and co-immunoprecipitated USP15 (A) or USP4 (B). (C) Heatmap representation of the signal intensities for co-precipitated proteins which satisfied the criteria of exhibiting a fold change >10 compared with negative control and not being a contaminant that interacted with anti-FLAG antibody (Mellacheruvu et al., 2013). The signal is calculated as the intensity ratio between the interactor and the product of the UbV bait and USP15, and the interactors are ranked based on average intensities across experiments. Known USP15 physical interactors based on Pathway Commons (Cerami et al., 2011) are shown in black and ubiquitin-related enzymes in red, and the full list of interactors can be found in Table S2.
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Isotope Products Laboratories 241am
Figure 3. Mass Spectrometry of Cellular Proteins Co-precipitated with UbVs (A and B) Mass spectrometry peak intensity ratios are shown (y axis) for immunoprecipitated UbVs (x axis) and co-immunoprecipitated USP15 (A) or USP4 (B). (C) Heatmap representation of the signal intensities for co-precipitated proteins which satisfied the criteria of exhibiting a fold change >10 compared with negative control and not being a contaminant that interacted with anti-FLAG antibody (Mellacheruvu et al., 2013). The signal is calculated as the intensity ratio between the interactor and the product of the UbV bait and USP15, and the interactors are ranked based on average intensities across experiments. Known USP15 physical interactors based on Pathway Commons (Cerami et al., 2011) are shown in black and ubiquitin-related enzymes in red, and the full list of interactors can be found in Table S2.
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Figure 3. Mass Spectrometry of Cellular Proteins Co-precipitated with UbVs (A and B) Mass spectrometry peak intensity ratios are shown (y axis) for immunoprecipitated UbVs (x axis) and co-immunoprecipitated USP15 (A) or USP4 (B). (C) Heatmap representation of the signal intensities for co-precipitated proteins which satisfied the criteria of exhibiting a fold change >10 compared with negative control and not being a contaminant that interacted with anti-FLAG antibody (Mellacheruvu et al., 2013). The signal is calculated as the intensity ratio between the interactor and the product of the UbV bait and USP15, and the interactors are ranked based on average intensities across experiments. Known USP15 physical interactors based on Pathway Commons (Cerami et al., 2011) are shown in black and ubiquitin-related enzymes in red, and the full list of interactors can be found in Table S2.
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resource source identifier antibodies anti cul5 rabbit bethyl  (Bethyl)
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(A) Affinity purification coupled to mass spectrometry (AP-MS) workflow for discovering Vif-dependent protein interactors of the <t>CUL5</t> E3 ligase complex.
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resource source identifier rat anti-tubulin bio-rad mca77g  (Bio-Rad)
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(A) Affinity purification coupled to mass spectrometry (AP-MS) workflow for discovering Vif-dependent protein interactors of the <t>CUL5</t> E3 ligase complex.
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Image Search Results


Figure 3. Mass Spectrometry of Cellular Proteins Co-precipitated with UbVs (A and B) Mass spectrometry peak intensity ratios are shown (y axis) for immunoprecipitated UbVs (x axis) and co-immunoprecipitated USP15 (A) or USP4 (B). (C) Heatmap representation of the signal intensities for co-precipitated proteins which satisfied the criteria of exhibiting a fold change >10 compared with negative control and not being a contaminant that interacted with anti-FLAG antibody (Mellacheruvu et al., 2013). The signal is calculated as the intensity ratio between the interactor and the product of the UbV bait and USP15, and the interactors are ranked based on average intensities across experiments. Known USP15 physical interactors based on Pathway Commons (Cerami et al., 2011) are shown in black and ubiquitin-related enzymes in red, and the full list of interactors can be found in Table S2.

Journal: Structure (London, England : 1993)

Article Title: Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15.

doi: 10.1016/j.str.2019.01.002

Figure Lengend Snippet: Figure 3. Mass Spectrometry of Cellular Proteins Co-precipitated with UbVs (A and B) Mass spectrometry peak intensity ratios are shown (y axis) for immunoprecipitated UbVs (x axis) and co-immunoprecipitated USP15 (A) or USP4 (B). (C) Heatmap representation of the signal intensities for co-precipitated proteins which satisfied the criteria of exhibiting a fold change >10 compared with negative control and not being a contaminant that interacted with anti-FLAG antibody (Mellacheruvu et al., 2013). The signal is calculated as the intensity ratio between the interactor and the product of the UbV bait and USP15, and the interactors are ranked based on average intensities across experiments. Known USP15 physical interactors based on Pathway Commons (Cerami et al., 2011) are shown in black and ubiquitin-related enzymes in red, and the full list of interactors can be found in Table S2.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-Ub P4D1 Santa Cruz Cat# sc-8017; RRID: AB_628423 anti-HA Y-11 Santa Cruz Cat# sc-805; RRID: AB_631618 anti-Myc 9E10 Santa Cruz Cat# sc-40; RRID: AB_627268 anti-TbR-I V-22 Santa Cruz Cat# sc-398; RRID: AB_632493 anti-TbR-I R-20 Santa Cruz Cat# sc-399; RRID: AB_632490 anti-MYC Sigma Cat# C3956; RRID: AB_439680 anti-b-actin Sigma Cat# A1978; RRID: AB_476692 anti-FLAG Sigma Cat# F7425/ F1804; RRID: AB_439687/AB_262044 anti-actin Millipore Cat# MAB1501; RRID: AB_2223041 anti-USP15 Abcam Cat# ab56900/ab97533; RRID: AB_946080/AB_10678830 anti-TRIM25 Proteintech Cat# 12573-1-AP; RRID: AB_2209732 anti-Xpress Life Technologies Cat# R910-25; RRID: AB_2556552 Bacterial and Virus Strains Escherichia coli: BL21 (DE3) NEB Cat# C2527I Chemicals, Peptides, and Recombinant Proteins USP15 full length Boston Biochem Cat# E-594 Ub-AMC Boston Biochem Cat# U-550 Ubiquitin-Rhodamine 110 Boston Biochem Cat# U-555 Critical Commercial Assays Simply P Total RNA extraction kit Bioflux Cat# BSC52S1 High Capacity cDNA Reverse Transcription kit Applied Biosystems Cat# 4368814 Dual luciferase system Promega Cat# E1910 Deposited Data USP15-DUSP/UbV.15.D structure This paper PDB: 6DJ9 USP15-D1D2/UbV.15.2 structure This paper PDB: 6CRN USP15-D1D2/UbV.15.1a structure This paper PDB: 6ML1 USP15-D1D2/UbV.15.1d structure This paper PDB: 6CPM Affinity-based mass spectrometry performed with UbVs This paper; ProteomeXchange Consortium PXD011840 Experimental Models: Cell Lines Human: HEK293T ATCC Cat# CRL-3216 Oligonucleotides shRNA targeting USP15: 50-GGAACACCTTATTGATGAA-30 This paper N/A qRT–PCR primers for SMAD7: 5’-AAACAGGGGGAACGA ATTATC-3’ and 5’-ACCACGCACCAGTGTGAC-3’ This paper N/A qRT–PCR primers for GAPDH: 50-AACAGCGACACCCAC TCCTC-30 and 50-CATACCAGGAAATGAGCTTGAC-30 This paper N/A Recombinant DNA pHH0103 GST-TEV-USP15 FLDinsert (1-471, 780-981) This paper N/A pHH0103 GST-TEV-USP15 CD (275-981) This paper N/A pHH0103 GST-TEV-USP15 D1D2 (275-471,780-981) This paper N/A pHH0103 GST-TEV-USP15 D1D2D1 (275-471,780-934) This paper N/A (Continued on next page) Structure 27, 1–16.e1–e5, April 2, 2019 e1

Techniques: Mass Spectrometry, Immunoprecipitation, Negative Control, Ubiquitin Proteomics

(A) Affinity purification coupled to mass spectrometry (AP-MS) workflow for discovering Vif-dependent protein interactors of the CUL5 E3 ligase complex.

Journal: Cell host & microbe

Article Title: ARIH2 is a Vif-dependent regulator of CUL5-mediated APOBEC3G degradation in HIV infection

doi: 10.1016/j.chom.2019.05.008

Figure Lengend Snippet: (A) Affinity purification coupled to mass spectrometry (AP-MS) workflow for discovering Vif-dependent protein interactors of the CUL5 E3 ligase complex.

Article Snippet: ​ 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 Trans IT-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?

Techniques: Affinity Purification, Mass Spectrometry

(A) Relative abundance comparison of all specific interactors for CUL5, CBFß, and ELOB, respectively, under HIV wt and HIV ΔVif infection conditions shown as volcano plots. Volcano plots describe the log2 fold change and −log10 p-value of each interactor comparing HIV wt to ΔVif infection as determined by MSstats (M. Choi et al., 2014). The dashed line represents a p-value cutoff of 0.05. Proteins indicated in red are significantly upregulated enriched under HIV wt infection (p-value cutoff 0.05, n = 4), protein indicated in black represent known bait interactors, while grey dots are all other interactors. Data has been acquired by a targeted proteomics strategy.

Journal: Cell host & microbe

Article Title: ARIH2 is a Vif-dependent regulator of CUL5-mediated APOBEC3G degradation in HIV infection

doi: 10.1016/j.chom.2019.05.008

Figure Lengend Snippet: (A) Relative abundance comparison of all specific interactors for CUL5, CBFß, and ELOB, respectively, under HIV wt and HIV ΔVif infection conditions shown as volcano plots. Volcano plots describe the log2 fold change and −log10 p-value of each interactor comparing HIV wt to ΔVif infection as determined by MSstats (M. Choi et al., 2014). The dashed line represents a p-value cutoff of 0.05. Proteins indicated in red are significantly upregulated enriched under HIV wt infection (p-value cutoff 0.05, n = 4), protein indicated in black represent known bait interactors, while grey dots are all other interactors. Data has been acquired by a targeted proteomics strategy.

Article Snippet: ​ 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 Trans IT-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?

Techniques: Infection

(A) Schematic of Vif recruitment of CBFß to the CUL5 E3 ligase complex for ubiquitination and degradation of APOBEC3G.

Journal: Cell host & microbe

Article Title: ARIH2 is a Vif-dependent regulator of CUL5-mediated APOBEC3G degradation in HIV infection

doi: 10.1016/j.chom.2019.05.008

Figure Lengend Snippet: (A) Schematic of Vif recruitment of CBFß to the CUL5 E3 ligase complex for ubiquitination and degradation of APOBEC3G.

Article Snippet: ​ 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 Trans IT-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?

Techniques:

(A) Workflow for functional validation of CUL5 factors using CRISPR knockouts followed by HIV infection in primary T cells, adapted from Hultquist et al (Hultquist et al., 2016).

Journal: Cell host & microbe

Article Title: ARIH2 is a Vif-dependent regulator of CUL5-mediated APOBEC3G degradation in HIV infection

doi: 10.1016/j.chom.2019.05.008

Figure Lengend Snippet: (A) Workflow for functional validation of CUL5 factors using CRISPR knockouts followed by HIV infection in primary T cells, adapted from Hultquist et al (Hultquist et al., 2016).

Article Snippet: ​ 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 Trans IT-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?

Techniques: Functional Assay, CRISPR, Infection

KEY RESOURCES TABLE

Journal: Cell host & microbe

Article Title: ARIH2 is a Vif-dependent regulator of CUL5-mediated APOBEC3G degradation in HIV infection

doi: 10.1016/j.chom.2019.05.008

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ 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 Trans IT-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?

Techniques: Recombinant, Magnetic Beads, Sequencing, Transfection, Protease Inhibitor, CRISPR, Software, Mass Spectrometry