KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-FLAG M2 | Sigma Aldrich | Cat#F1804; RRID: AB_262044 |
| Anti-HIV Nef Polyclonal | NIH AIDS Reagent Program | Cat#2949; RRID: n/a. |
| Anti-HA-HRP | Sigma Aldrich | Cat#H6533-1VL; RRID: AB_439706 |
| Anti-FLAG-HRP | Sigma Aldrich | Cat#A8592-.2MG; RRID: AB_262044 |
| Anti-Actin-HRP | Sigma Aldrich | Cat#A3854-200UL; RRID: AB_262011 |
| Anti-GAPDH-HRP | Proteintech | Cat#HRP-60004; RRID: AB_2107436 |
| Rabbit polyclonal anti-CrkRS (CDK12) | Novus | Cat#NB100-87011; RRID: AB_1199396 |
| Rabbit polyclonal anti-CDC2L5 (CDK13) | Novus | Cat#NB100-68268; RRID: AB_1107830 |
| Rabbit polyclonal anti-Cyclin K | Abcam | Cat#Ab85854; RRID: AB_1860218 |
| Goat-anti-human-IgG-HRP | Thermo Fisher | Cat#31412; RRID: AB_228265 |
| Goat-anti-rabbit-IgG-HRP | Thermo Fisher | Cat#G21234; RRID: AB_2536530 |
| Goat-anti-mouse-IgG-HRP | Thermo Fisher | Cat#G21040; RRID: AB_2536527 |
| AF647 anti-HA | BioLegend | Cat#682404; RRID: AB_2566616 |
| Pacific Blue anti-HA | BioLegend | Cat#901525; RRID: AB_2734659 |
| Monoclonal anti-Nef | Zheng et al., 2003 | n/a |
| Bacterial and virus strains | ||
| HIV-1 Provirus pH22, pH22ΔN | Zheng et al., 2003 | n/a |
| BL21 E. coli | NEB | Cat#C2530H |
| DH10B E. coli | NEB | Cat#C3019H |
| HB101 E. coli | Promega | Cat#L2011 |
| Chemicals, peptides, and recombinant proteins | ||
| Propidum Iodide Cell Cycle Reagent | Thermo Fisher | Cat#BMS500PI |
| MG132 | APExBio | Cat#A2585 |
| Lactacystin | Enzo | Cat#BML-P1104-0200 |
| Bafilomycin A1 | APExBio | Cat#A8627 |
| NH4Cl | Sigma | Cat#A9434-500G |
| THZ531 | APExBio | Cat#A8736 |
| Protease Inhibitor Cocktail | Sigma | Cat#P8340 |
| FCFSPGGEDKEEQQPGK (T366K mutant) | GenScript | n/a |
| FCFSPGGEDTEEQQPGK | GenScript | n/a |
| FCF{pSer}PGGEDTEEQQPGK | GenScript | n/a |
| 3X FLAG peptide | Sigma | Cat#F4799-4MG |
| Critical commercial assays | ||
| CloneExpressII one-step cloning kit | Vazyme Biotech, China | Cat#C112 |
| Site-directed Mutagenesis Kit | Agilent | Cat#200521 |
| Firefly Luciferase Assay Kit | Biotium | Cat#30085-T |
| Phos-Tag Phosphoprotein Gel Stain Kit | ABP Biosciences | Cat#P005A |
| Pierce Classic IP Kit | Thermo Fisher | Cat#26146 |
| Experimental models: Cell lines | ||
| HEK293T | ATCC | CRL-3216 |
| TZM-bI | NIH AIDS Research and Reference Reagent Program | 8129 |
| SERINC3/5 knockout Jurkat-TAg | A gift from Heinrich Gottlinger, University of Massachusetts | n/a |
| Oligonucleotides | ||
| CCNK gRNA (5′-AGGACTTGATCCAGCCA CCGAGG-3′) (pGEM-T) | Promega | n/a |
| Recombinant DNA | ||
| pCMV6-Ser5-FLAG | Ahmad et al., 2019; Shi et al., 2018; Zhang et al., 2017 | n/a |
| pCMV6-CD4-FLAG | Ahmad et al., 2019; Shi et al., 2018; Zhang et al., 2017 | n/a |
| pBJ5-Ser5-HA | A gift from Heinrich Gottlinger, University of Massachusetts | n/a |
| pBJ5-iHA-Ser5 | A gift from Heinrich Gottlinger, University of Massachusetts | n/a |
| pcDNA3.1-CDK12-FLAG | A gift from Qintong Li, Sichuan University | n/a |
| pcDNA3.1-CDK13-FLAG | A gift from Qintong Li, Sichuan University | n/a |
| prEF-FLAG-CCNK | A gift from Qintong Li, Sichuan University | n/a |
| pLKO.1-CCNKshRNA | A gift from Qintong Li, Sichuan University | n/a |
| pLKO.1-CDK12shRNA | A gift from Qintong Li, Sichuan University | n/a |
| pLKO.1-CDK13shRNA | A gift from Qintong Li, Sichuan University | n/a |
| pCMV6-CCNK-FLAG | Origene | n/a |
| pMJ920 (GFP marker) | Jinek et al., 2013 | Jennifer Doudna, UC Berkeley, Addgene Cat#42234 |
| pcDNA3.1-CDK12-HA | This paper | n/a |
| pcDNA3.1-CDK13-HA | This paper | n/a |
| pGEX-ICL4 | This paper | n/a |
| pCMV6-Ser5-FLAG S249A, S360A, T366A, L350A/I352A | This paper | n/a |
| pBJ5-iHA-Ser5 S249A, S360A, T366A, L350A/I352A, L350A/I352A/S360D | This paper | n/a |
| pGEX-ICL4 S360A | This paper | n/a |
| pcDNA3.1-CDK12-FLAG D858A, D876N, D858A/D876N | This paper | n/a |
| pcDNA3.1-CDK13-FLAG D837A, D855N, D837A/D855N | This paper | n/a |
| pTWIST-CD8α-ICL4 and mutants | TWIST Bioscience | n/a |
| pNL4.3-LL-AA | A gift from Warner Greene, UCSF | n/a |
| Software and algorithms | ||
| ModFit LT version 4.1.7 | Verity | https://www.vsh.com/products/mflt/mfTrialVersions.asp |
| Proteome Discoverer 2.2 + SEQUEST HT Search Engine | Thermo Fisher OPTON-30945 | https://www.thermofisher.com/order/catalog/product/OPTON-30945#/OPTON-30945 |
| MassHunter Qualitative Analysis Navigator B.08.00 | Agilent | https://www.agilent.com/en/support/software-informatics/qual-b-0800-sp1 |
| FlowJo v10.7 | FlowJo | https://www.flowjo.com/solutions/flowjo/downloads |
| Other | ||
| Zip-tip | Millipore | Cat#ZTC18S096 |
| EASY nanoLC-1200 system | Thermo Fisher | Cat#LC140 |
| Protein G beads | Thermo Fisher | Cat#20398 |
| Anti-HA Affinity Matrix | Sigma | Cat#11815016001 |
| Anti-FLAG M2 Affinity Gel | Sigma | Cat#A2220 |