REAGENT or RESOURCE Antibodies	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-FLAG M2	Sigma-Aldrich	Cat# F1804; RRID:AB_262044
Mouse monoclonal anti-hemagglutinin (HA)	Sigma-Aldrich	Cat# H3663; RRID:AB_262051
Mouse monoclonal anti-Cyclophilin A (human)	Abcam	Cat# ab58144; RRID:AB_941220
Rabbit monoclonal anti-TRIM5a (human, monkey)	Cell Signaling Technology	Cat# 14326S; RRID:AB_2798451
Mouse monoclonal anti-glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	Invitrogen (Thermo Fisher Scientific)	Cat# AM4300; RRID:AB_437392
Mouse monoclonal anti-HIV-1 p24 (183-H12-5C)	NIH AIDS Reagent Program	Cat# 3637; RRID:CVCL_9N48
Goat anti-Mouse IRDye 680LT	LI-COR	Cat# 925–68020; RRID:AB_2687826
Goat anti-Rabbit IRDye 680LT	LI-COR	Cat# 926–68021; RRID:AB_10706309
Goat anti-Mouse IRDye 800CW	LI-COR	Cat# 926–32210; RRID:AB_621842
Goat anti-Rabbit IRDye 800CW	LI-COR	Cat# 925–32211; RRID:AB_2651127
Rabbit monoclonal anti-glyceraldehyde-3-phosphate dehydrogenase (GAPDH)	Cell Signaling Technology	Cat #2118S; RRID:AB_437392
Bacterial and Virus Strains
E. Coli one-shoot BL21star (DE3)	Invitrogen	Cat#C601003
E. Coli DH5α competent cells	Zymo Research	Cat# T3007
N-MLV	Diaz-Griffero et al., 2008	N/A
B-MLV	Diaz-Griffero et al., 2008	N/A
HIV-1 NL4-3	This paper	N/A
HIV-1-G89V	This paper	N/A
HIV-1-P90A	This paper	N/A
HIV-1-A92E	This paper	N/A
HIV-1-G94D	This paper	N/A
HIV-1 NL4-3 Nef:IRES:GFP	Hultquist et al., 2016	N/A
Biological Samples
Healthy adult Peripheral Blood Mononuclear Cells (PBMCs)	LifeSource/Vitalant	N/A
Chemicals, Peptides, and Recombinant Proteins
Cyclosporin A	Millipore Sigma	Cat#: PHR1092; CAS: 59865-13-3
Dimethyl sulfoxide (DMSO)	Sigma-Aldrich	Cat#: D2438; CAS: 67-68-5
Difco LB Broth, Miller (Luria-Bertani)	Fisher Scientific	Cat#: BD244610
Isopropyl β-D-1-thiogalactopyranoside	Sigma-Aldrich	Cat#: I5502; CAS: 367-93-1
cOmplete EDTA-free protease inhibitor cocktail	Millipore Sigma	Cat#: 11873580001,
Tris (TRIS(HYDROXYMETHYL)AMINOMETHANE)	Crystalgen	Cat#300-844-5000; CAS: 77-86-1
Sodium Chloride (NaCl)	Crystalgen	Cat# 300-747-5000; CAS: 767-14-5
β-Mercaptoethanol (BME)	Acros organics	Cat# 125470010; CAS: 60-24-2
2-(N-morpholino) ethanesulfonic acid (MES)	Calbiochem	Cat# 475893; CAS: 4432-31-9
Magnesium Chloride (MgCl2)	Sigma-Aldrich	Cat# M2670; CAS: 7791-18-6
Potassium Chloride (KCl)	Fisher Scientific	Cat# BP366-1; CAS: 7447-40-7
Dithiothreitol (DTT)	VWR	Cat# 97061-340; CAS: 3483-12-3
D-(+)-Sucrose	VWR	Cat# 97061-432; CAS: 57-50-1
Human IL-2	Cell Signaling Technology	Cat# 8907SF
Phytohemagglutinin-L (PHA-L)	Millipore Sigma	Cat# 11249738001
Human IL-2	MACS Miltenyi Biotec	Cat# 130-097-742
Anti-Human CD3 (UCHT1)	Tonbo Biosciences	Cat# 70-0038-U100; RRID:AB_2621475
Anti-Human CD28 (CD28.2)	Tonbo Biosciences	Cat# 70-0289-U100; RRID:AB_2621493
Cas9-NLS Recombinant Protein, purified, 40uM	MacroLab Berkeley	N/A
Dulbecco’s Phosphate-Buffered Salt (PBS) Solution 1X	Corning	21031CV
EDTA, pH 8.0, 0.5M	Corning	46034CI
Critical Commercial Assays
QuikChange II site-directed mutagenesis kit	Agilent	Cat#: 200523
CD4+ T Cell Isolation Kit, human	MACS Miltenyi Biotec	Cat# 130-096-533
EasySep Human CD4+ T Cell Isolation Kit	STEMCELL	Cat# 17952
P3 Primary Cell 96-well Nucleofector Kit	Lonza	Cat# V4SP-3096
T Cell Activation/Expansion Kit, human	MACS Miltenyi Biotec	Cat# 130-091-441
QIAamp DNA Micro Kit	QIAGEN	Cat# 56304
Experimental Models: Cell Lines
Human: Jurkat E6.1	ATCC	TIB-152
Human: 293T/17	ATCC	CRL-11268
Human: HT1080	ATCC	CCL-121
Oligonucleotides
All standard cloning primers for site-directed mutagenesis	Integrated DNA Technologies	N/A
Early reverse transcripts (ERT) hRU5-F, 5′-GCCTCAATAAAGCTTGCCTTGA-3′	Mbisa et al., 2009	N/A
Early reverse transcripts (ERT) hRU5-R, 5′-TGACTAAAAGGGTCTGAGGGATCT-3′	Mbisa et al., 2009	N/A
ERT probe, 5′-(FAM)-AGAGTCACACAAC AGACGGGCACACACTA-(TAMRA)-3′	Mbisa et al., 2009	N/A
Late Reverse Transcripts (LTR) MH531, 5′-TGTGTGCCCGTCTGTTGTGT-3′,	Butler et al., 2001	N/A
Late Reverse Transcripts (LTR) MH532, 5′-GAGTCCTGCGTCGAGAGAGC-3′	Butler et al., 2001	N/A
LRT-Probe, 5′-(FAM)-CAGTGGCGCCCGAACAGGGA-(TAMRA)-3′	Butler et al., 2001	N/A
2-LTR circles MH535, 5′-AACTAGGGAACCCACTGCTTAAG-3′	Butler et al., 2001	N/A
2-LTR circles MH536, 5′-TCCACAGATCAAGGATATCTTGTC-3’	Butler et al., 2001	N/A
2-LTR probe MH603, 5′-(FAM)-ACACTAC TTGAAGCACTCAAG-GCAAGCTTT-(TAMRA)-3′	Butler et al., 2001	N/A
Table S1 Primers and RNA guides	N/A	N/A
Recombinant DNA
pET-11a	EMD Mollipore	Cat # 69436
Plasmid: CA A14C/E45C in pET-11a	Selyutina et al., 2018	N/A
Plasmid: CA A14C/E45C/P90A in pET-11a	Selyutina et al., 2018	N/A
Plasmid: CA A14C/E45C/A92E in pET-11a	This paper	N/A
Plasmid: CA A14C/E45C/G94D in pET-11a	This paper	N/A
pLKO1	Sigma	Cat# 10878
pLKO1-shRNA-TRIM5ahu	Sigma	Cat# 13478
Plasmid: human TRIM5a-HA in pLPCX	Perron et al., 2007	N/A
Plasmid: rhesus TRIM5a-HA in pLPCX	Stremlau et al., 2006a	N/A
Plasmid: Tat	Stremlau et al., 2006a	N/A
Plasmid: Rev	Stremlau et al., 2006a	N/A
Plasmid: VSVg	Stremlau et al., 2006	N/A
Other
HiTrap Q HP 5mL	GE Healthcare	Cat# 17115401
HiTrap SP HP 5mL	GE Healthcare	Cat# 17115201
Centriprep Centrifugal Filter Unit 30 kDa	Millipore Sigma	Cat# 4306
SnakeSkin Dialysis Tubing, 10KMWCO	Fisher Scientific	Cat# 68100
GE Healthcare Ficoll-Paque PLUS Media	Fisher Scientific	Cat# 45001-749
Hanks’ Balanced Salt solution	Sigma-Aldrich	Cat# H6648
LS Columns	MACS Miltenyi Biotec	Cat# 130-042-401
MS Columns	MACS Miltenyi Biotec	Cat# 130-042-201
SepMate PBMC Isolation Tubes	STEMCELL	Cat# 85450
Maxima Probe/ROX qPCR Master Mix (2X)	ThermoScientific	Cat#K0231
TURBO DNase (2 U/μL)	Invitrogen	Cat#AM2238
Platinum SuperFi DNA Polymerase	Invitrogen	Cat#12351050
iTaq Universal SYBR® Green Supermix	Biorad	Cat#1725124
0.2 ml PCR 8-tube with attached clear flat caps, natural	USA Scientific	1402–3900
Fetal Bovine Serum (FBS, heat-inactivated)	GIBCO	16140–071
RPMI-1640 (high glucose)	Corning	MT10-017-CV
Penicillin-streptomycin (5 mg/mL)	Corning	MT10-040-CV
Sodium pyruvate (100×)	Corning	MT25-000-CI
HEPES (100×)	Fisher / HyClone	SH3023701
DMEM (high glucose)	Corning	MT10-017-CV