KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit monoclonal anti-HsClpP | Abcam | RRID:AB_124822 |
| Rabbit monoclonal anti-HsClpX | Abcam | RRID:AB_168338 |
| Rabbit monoclonal anti-Mcl1 | Cell Signaling Technology | RRID:AB_2799149 |
| Rabbit monoclonal anti-Caspase 8 | Cell Signaling Technology | RRID:AB_10545768 |
| Rabbit monoclonal anti-Caspase 9 | Cell Signaling Technology | RRID:AB_2068621 |
| Rabbit polyclonal anti-TFAM | Proteintech | RRID:AB_11182588 |
| Rabbit polyclonal anti-Grp75 | Proteintech | RRID:AB_2120458 |
| Goat monoclonal anti-Caspase 3 | R&D Biosystems | RRID:AB_354518 |
| Mouse monoclonal anti-GAPDH | Abcam | RRID:AB_8245 |
| HRP-conjugated goat anti-rabbit IgG | BioRad | RRID:AB_11125142 |
| HRP-conjugated goat anti-mouse IgG | BioRad | RRID:AB_11125547 |
| HRP-conjugated rabbit anti-goat IgG | Sigma-Aldrich | RRID:AB_258242 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Sodium acetate, ACS Reagent, ≥ 99.0% | Sigma-Aldrich | Cat#241245 |
| PEG 4,000, powder | Sigma-Aldrich | Cat#8.17006 |
| TR-27 | reference19 | N/A |
| TR-57 | reference19 | N/A |
| TR-65 | reference19 | N/A |
| TR-107 | This paper | N/A |
| TR-133 | This paper | N/A |
| ADEP-14 | reference6 | N/A |
| Doxorubicin (hydrochloride) | Cayman Chemical Co. | Cat#15007 |
| Sulforhodamine B (SRB) | Sigma-Aldrich | Cat#230162 |
| jetPRIME Transfection Reagent | Polyplus Transfection | Cat#114–07 |
| jetPRIME Transfection Buffer | Polyplus Transfection | Cat#712–60 |
| Reprosil-Pur 120 C18-AQ, 1.9 μm | Dr. Maisch | Cat#r119.aq. |
| Casein-FITC | Sigma-Aldrich | Cat# C3777 |
| Untagged human mitochondrial ClpP | This paper | N/A |
| Yeast SUMO protease | reference52 | N/A |
| Critical Commercial Assays | ||
| PureLink Quick Plasmid Miniprep Kit | Thermo-Fisher Scientific | Cat#K210011 |
| Pierce BCA Protein Assay Kit | Thermo-Fisher Scientific | Cat#23225 |
| Deposited Data | ||
| Structure of human ClpP complex with ADEP-28 | Protein Data Bank reference6 | 6BBA |
| Structure of human ClpP complex with ONC201 | Protein Data Bank reference8 | 6DL7 |
| Structure of human ClpP complex with ZG111 | Protein Data Bank reference34 | 7VP9 |
| Structure of human ClpP Y118A mutant complex with D9 | Protein Data Bank reference7 | 6H23 |
| Structure of human ClpP complex with TR-27 | Protein Data Bank (This paper) | 7UVM |
| Structure of human ClpP complex with TR-57 | Protein Data Bank (This paper) | 7UVN |
| Structure of human ClpP complex with TR-65 | Protein Data Bank (This paper) | 7UVR |
| Structure of human ClpP complex with TR-107 | Protein Data Bank (This paper) | 7UVU |
| Structure of human ClpP complex with TR-133 | Protein Data Bank (This paper) | 7UW0 |
| HYTANE data | MassIVE repository (This paper) | MSV000089642 |
| Experimental Models: Cell Lines | ||
| HEK293 T-REx | Gift from A. Trifunovic | RRID:CVCL_U427 |
| HEK293 T-RExCLPP−/− | reference53 | N/A |
| HEK293 T-RExCLPX−/− | reference6 | N/A |
| MDA-MB-231 | Gift from L. Attisano | RRID:CVCL_0062 |
| MDA-MB-231 CLPP−/− | This paper | N/A |
| MDA-MB-231 CLPX−/− | This paper | N/A |
| Experimental Models: Organisms / Strains | ||
| Escherichia coli DH5α | Lab stock | NCBI:txid668369 |
| Escherichia coli BL21(DE3) ΔclpP::cat (SG1146) | reference54 | N/A |
| Oligonucleotides | ||
| CLPP Exon 1 pX330 F: CACCGAAGCCGACCGGGGCGTGCGG |
This paper | N/A |
| CLPP Exon 1 pX330 R: AAACCCGCACGCCCCGGTCGGCTTC |
This paper | N/A |
| CLPP Exon 1 ssODN: GCATGACGCCACCCGGGCCCCCCCTACCAATATTCATTATTATCACCTTCCGCACGCCCCGGTCGGCTTCCGTCCGATGGCGGAACTACAGCTTCCGGCG |
This paper | N/A |
| CLPX Exon1 pX330 F: CACCGCGGTGCTTGTACTTGCGGCG |
reference6 | N/A |
| CLPX Exon1 pX330 R: AAACCGCCGCAAGTACAAGCACCGC |
reference6 | N/A |
| CLPX Exon1 ssODN: GGCCTCGCGGAGATGCCCAGCTGCGGTGCTTGTACTTGCGGCGCGGCGTAGGTCCGGCTCATCACCTCCTCACTCGCCTCCGCGCAGAGA |
reference6 | N/A |
| Recombinant DNA | ||
| pX330 | reference48 | RRID:Addgene_42230 |
| pX330-CLPP KO | This paper | N/A |
| pX330-CLPX KO | reference6 | N/A |
| pETSUMO2-CLPP(-MTS) | reference6 | N/A |
| pETSUMO2-TFAM(-MTS) | This paper | N/A |
| Software and Algorithms | ||
| Proteome Discoverer 2.2 | Thermo-Fisher Scientific | RRID:SCR_014477 |
| WebLogo 2.8.2 | reference44 | RRID:SCR_010236 |
| AlphaFold | reference39 | N/A |
| NIS-Elements Basic Research Software | Nikon | RRID:SCR_002776 |
| XDS | reference55 | https://xds.mr.mpg.de/ |
| Phenix | reference46 | https://phenix-online.org/ |
| COOT | reference45 | http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot |
| PISA | reference47 | https://www.ebi.ac.uk/pdbe/pisa/ |
| The PyMOL Molecular Graphics System | Schrödinger, LLC | https://pymol.org/2/ |
| Other | ||
| BbsI | New England Biolabs | Cat#R0539S |
| FastAP | Thermo-Fisher Scientific | Cat#EF0651 |
| T4 Polynucleotide Kinase | New England Biolabs | Cat#M0201S |
| T4 DNA Ligase | New England Biolabs | Cat#M0202S |
| EnSpire 2300 Multilabel Reader | Perkin-Elmer | Cat#655077 |
| P-2000 Laser-Based Micropipette Puller | Sutter Instrument Co. | Cat#P-2000 |
| EkspertNanoLC 425 HPLC System | Eksigent Technologies | Cat#Ekspert425 |
| Orbitrap Fusion Lumos Tribrid Mass Spectrometer | Thermo-Fisher Scientific | Cat#IQLAAEGAAPF ADBMBHQ |
| Microcon-10kDa Ultracel YM-10 filter unit | Millipore | Cat#Z648078 |
| C18 Stage Tips | Supelco | Cat#66883-U |
| Eclipse 80i fluorescence microscope | Nikon | RRID:SCR_015572 |
| X-Cite Series 120Q excitation light source | Excelitas Technologies | https://www.excelitas.com/product/x-cite-120q |