Reagents and tools table
| Reagent/resource | Reference or source | Identifier or catalog number |
|---|---|---|
| Bacterial strains | ||
| E. coli DH5α | Invitrogen | 18265017 |
| E. coli BL21(DE3) | Merck Australia | CMC0016 |
| Antibodies | ||
| BNIP3 (ANa-40) mouse monoclonal | Santa Cruz Biotechnology | sc-56167 |
| BNIP3 rabbit monoclonal | Abcam | ab109362 |
| Cullin 1 rabbit | Invitrogen | 718700 |
| FLAG monoclonal | Sigma-Aldrich | F3165 |
| FLAG rabbit polyclonal | Sigma-Aldrich | SAB4301135 |
| GFP | Invitrogen | MA5-15256 |
| HA rabbit monoclonal | Cell Signalling Technology | 3724S |
| HDAC6 | Santa Cruz Biotechnology | sc-11420 |
| HIF1α rabbit monoclonal | Cell Signalling Technology | 36169S |
| MTCO2 mouse monoclonal | Abcam | ab110258 |
| MYC | Bethyl Technologies | A190-105A |
| NIX mouse monoclonal | Santa Cruz Technologies | sc-166332 |
| NIX rabbit polyclonal | Cell Signalling Technology | 12396 |
| p27 mouse monoclonal | BD Biosciences | 610242 |
| PPTC7 rabbit | Novus Biologicals | NBP1-90654 |
| Skp1 | Pagano Laboratory | |
| TOMM20 mouse monoclonal | BD Biosciences | Clone 29 612278 |
| HSP60 | ||
| Vinculin (VCL) mouse monoclonal | Santa Cruz Biotechnology | sc-55465 |
| Donkey anti-mouse IgG Alexa FluorTM 488 | Invitrogen | A21202 |
| Donkey anti-mouse IgG Alexa FluorTM 555 | Invitrogen | A31570 |
| Donkey anti-mouse IgG Alexa Fluor TM 647 | Invitrogen | A31571 |
| Donkey anti-rabbit IgG Alexa FluorTM 488 | Invitrogen | A21026 |
| Donkey anti-rabbit IgG Alexa FluorTM 555 | Invitrogen | A31572 |
| Donkey anti-rabbit IgG Alexa FluorTM 647 | Invitrogen | A31573 |
| Chemicals | ||
| Benzamidine hydrochloride hydrate | Sigma-Aldrich | B6506 |
| Deoxyribonuclease I (DNase I) | Sigma-Aldrich | DN25 |
| Talon® resin | Clontech | 635503 |
| Glutathione Sepharose 4B | GE Healthcare | GEHE17-0756-0 |
| Isopropyl β-D-1-thiogalactopyranoside | Bioline | BIO-37036 |
| Recombinant DNA | ||
| PPTC7-1_pLentiCRISPR v2 | This paper | |
| PPTC7-2_pLentiCRISPR v2 | This paper | |
| Fbxl4 CRISPR guide RNA 2_pSpCas9 BB-2A-Puro (PX459) v2.0 | Nguyen-Dien | |
| hPPTC7_pcDNA3.1(+)-C-DYK | This paper | |
| hPPTC7-pcDNA3.1-FLAG | Natalie Niemi | |
| pLV[Exp]-Puro-EF1A>hPPTC7[NM_139283.2]/HA | This paper | |
| FBXL4-pcDNA3.1-3XFLAG | This paper | |
| D290N_hPPTC7_pcDNA3.1(+)-C-DYK | This paper | |
| D223N_hPPTC7_pcDNA3.1(+)-C-DYK | This paper | |
| D78N_hPPTC7_pcDNA3.1(+)-C-DYK | This paper | |
| pLV_Puro_EF1A_PPTC7_FLAG | This paper | |
| D78N_pLV_Puro_EF1A_PPTC7_FLAG | This paper | |
| D223N_pLV_Puro_EF1A_PPTC7_FLAG | This paper | |
| D290N_pLV_Puro_EF1A_PPTC7_FLAG | This paper | |
| D78A_hPPTC7_pcDNA3.1(+)-C-DYK | This paper | |
| D78A/D223A_hPPTC7_pcDNA3.1(+)-C-DYK | This paper | |
| D223A_D78A_pLV_Puro_EF1A_PPTC7_HA | This paper | |
| D78A_pLV_Puro_EF1A_PPTC7_HA | This paper | |
| K130E_hPPTC7_pcDNA3.1(+)-C-DYK | This paper | |
| Q128R_hPPTC7_pcDNA3.1(+)-C-DYK | This paper | |
| Y179D_hPPTC7_pcDNA3.1(+)-C-DYK | This paper | |
| N181E_hPPTC7_pcDNA3.1(+)-C-DYK | This paper | |
| Q128R_pLV_Puro_EF1A_PPTC7_HA | This paper | |
| K130E_pLV_Puro_EF1A_PPTC7_HA | This paper | |
| Y179D_pLV_Puro_EF1A_PPTC7_HA | This paper | |
| N181E_pLV_Puro_EF1A_PPTC7_HA | This paper | |
| NIX-RPE-AAA | This paper | |
| NIXD140-150 | This paper | |
| M71E_pLV_FBXL4_HA_WT_VB3 | This paper | |
| Arg544E_pLV_FBXL4_HA_WT_VB3 | This paper | |
| M71E and Arg544E_pLV_FBXL4_HA_WT_VB3 | This paper | |
| pLVX TetOne BNIP3 | This paper | |
| pLVX TetOne NIX | This paper | |
| Plasmid: pGEX-6P-2 | Cytiva | 28-9545-50 |
| Plasmid: pGEX-6P-2 GST-PPTC7(31-304) | This study | N/A |
| Plasmid: pGEX-6P-2 GST-PPTC7(31-304)(D290N) | This study | N/A |
| Deposited Data | ||
| SCFβTRPC (crystal structure) | RSCB Protein Data Bank | PDB ID: 6TTU |
| Human PPTC7 (protein sequence) | Uniprot | Q8NI37 |
| Human FBXL4 (open reading frame) | Uniprot | Q9UKA2 |
| Human BNIP3 (protein sequence) | Uniprot | Q12983 |
| Human NIX (protein sequence | Uniprot | O60238 |
| Software | ||
| Pymol | Schrodinger, USA | https://pymol.org/2/ |
| Consurf | Simpson et al, 2021 | https://consurf.tau.ac.il/consurf_index.php |
| AlphaFold2 Multimer | Sowter et al, 2001; Stojanovski et al, 2007 | https://github.com/deepmind/alphafold |
| ColabFold and ColabFold batch | Sun et al, 2024 | https://github.com/sokrypton/ColabFold |
| Other | ||
| HiLoadTM Superdex75 PG | GE Healthcare | Catalogue: 28989333 |