Appendix 1—key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Antibody | Mouse monoclonal α-α-synuclein (SYN211) | ThermoFisher Scientific | AHB0261; RRID:AB_10978319 | (1:500 dilution) |
| Antibody | Rabbit polyclonal α-CLPB (Skd3) | abcam | ab235349; RRID:AB_2847899 | (1:1000 dilution) |
| Antibody | Rabbit polyclonal α-CLPB (Skd3) | abcam | ab76179; RRID:AB_1310087 | (1:1000 dilution) |
| Antibody | Rabbit polyclonal α-CLPB (Skd3) | abcam | ab87253; RRID:AB_1952530 | (1:1000 dilution) |
| Antibody | Rabbit polyclonal α-CLPB (Skd3) | Proteintech | 15743–1-AP; RRID:AB_2847900 | (1:1000 dilution) |
| Antibody | Mouse monoclonal α-COXIV |
abcam | ab14744; RRID:AB_301443 | (1:1000 dilution) |
| Antibody | Mouse monoclonal α-GAPDH | abcam | ab8245; RRID:AB_2107448 | (1:1000 dilution) |
| Antibody | Rabbit polyclonal α-HAX1 | abcam | ab137613; RRID:AB_2847902 | (1:500 dilution) |
| Antibody | Rabbit polyclonal α-MICU2 |
abcam | ab101465; RRID:AB_10711219 | (1:1000 dilution) |
| Antibody | IRDye 680RD Goat anti-Rabbit IgG Secondary Antibody | Li-Cor | 926–68071; RRID:AB_10956166 | (1:2500 dilution) |
| Antibody | IRDye 800CW Goat anti-Mouse IgG Secondary Antibody | Li-Cor | 926–32210; RRID:AB_621842 | (1:2500 dilution) |
| Cell line (Escherichia coli) | BL21-CodonPlus (DE3) -RIL competent cells |
Agilent | 230245 | Chemically competent cells |
| Cell line (Homo sapiens) | Human HAP1 Knockout Cell Lines - WT | Horizon Discovery | HZGHC81570;; RRID:CVCL_Y019 | Human control cell line. The HAP1 cell line was bought directly from Horizon Discovery and has been control quality checked by the vendor. |
| Cell line (Homo sapiens) | Human HAP1 Knockout Cell Lines - CLPB | Horizon Discovery | HZGHC007326c001 | Human knockout cell line. The HAP1 ClpB knockout cell line was bought directly from Horizon Discovery and has been control quality checked by the vendor. |
| Commercial assay or kit | ATPase Activity Kit (Colorimetric) | Innova Biosciencens | 601–0120 | |
| Commercial assay or kit | Luciferase Assay Reagent | Promega | E1483 | |
| Chemical compound, drug | Creatine phosphate | Roche | 10621722001 | |
| Chemical compound, drug | ADP | MP Biomedicals | 150260 | |
| Chemical compound, drug | AMPPNP | Roche | 10102547001 | |
| Chemical compound, drug | ATP | Sigma-Aldrich | A3377 | |
| Chemical compound, drug | ATPγS | Roche | 10102342001 | |
| Chemical compound, drug | cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail | Sigma-Aldrich | 4693159001 | |
| Chemical compound, drug | Pepstatin A, microbial,≥90% (HPLC) | Sigma-Aldrich | P5318 | |
| Chemical compound, drug | Protease Inhibitor Cocktail (mammalian) | Sigma-Aldrich | P8340 | |
| Gene (Homo sapiens) | CLPB | NA | HGNC:30664 | |
| Peptide, recombinant protein | α-synuclein fibrils | Luk et al., 2012 | Preformed α-synuclein fibrils were a gift from Kelvin Luk. | |
| Peptide, recombinant protein | β-casein | Sigma-Aldrich | C6905 | |
| Peptide, recombinant protein | Creatine kinase | Roche | 10127566001 | |
| Peptide, recombinant protein | Firefly luciferase | Sigma-Aldrich | L9506 | |
| Peptide, recombinant protein | Hdj1 | Michalska et al., 2019 | ||
| Peptide, recombinant protein | Hsc70 | Michalska et al., 2019 | ||
| Peptide, recombinant protein | Hsp104 | DeSantis et al., 2012 and Jackrel et al., 2014 | ||
| Peptide, recombinant protein | Lysozyme | Sigma-Aldrich | L6876 | |
| Peptide, recombinant protein | MPPSkd3 | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Peptide, recombinant protein | MPPSkd3K387A | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Peptide, recombinant protein | MPPSkd3E455Q | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Peptide, recombinant protein | MPPSkd3Y430A | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Peptide, recombinant protein | PARLSkd3 | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Peptide, recombinant protein | PARLSkd3K387A | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Peptide, recombinant protein | PARLSkd3E455Q | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Peptide, recombinant protein | PARLSkd3Y430A | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Peptide, recombinant protein | PARLSkd3T268M | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Peptide, recombinant protein | PARLSkd3R475Q | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Peptide, recombinant protein | PARLSkd3A591V | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Peptide, recombinant protein | PARLSkd3R650P | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Peptide, recombinant protein | Skd3ANK | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Peptide, recombinant protein | Skd3NBD | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Recombinant DNA reagent | Hdj1 in pE-SUMO | Michalska et al., 2019 | ||
| Recombinant DNA reagent | Hsc70 in pE-SUMO | Michalska et al., 2019 | ||
| Recombinant DNA reagent | Hsp104 in pNOTAG | DeSantis et al., 2012 and Jackrel et al., 2014 | ||
| Recombinant DNA reagent | MPPSkd3 in pMAL C2 with TEV site | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Recombinant DNA reagent | MPPSkd3K387A in pMAL C2 with TEV site | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Recombinant DNA reagent | MPPSkd3E455Q in pMAL C2 with TEV site | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Recombinant DNA reagent | MPPSkd3Y430A in pMAL C2 with TEV site | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Recombinant DNA reagent | PARLSkd3 in pMAL C2 with TEV site | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Recombinant DNA reagent | PARLSkd3K387A in pMAL C2 with TEV site | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Recombinant DNA reagent | PARLSkd3E455Q in pMAL C2 with TEV site | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Recombinant DNA reagent | PARLSkd3Y430A in pMAL C2 with TEV site | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Recombinant DNA reagent | PARLSkd3T268M in pMAL C2 with TEV site | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Recombinant DNA reagent |
PARLSkd3R475Q in pMAL C2 with TEV site |
This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Recombinant DNA reagent | PARLSkd3A591V in pMAL C2 with TEV site | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Recombinant DNA reagent | PARLSkd3R650P in pMAL C2 with TEV site | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Recombinant DNA reagent | Skd3ANK in pMAL C2 with TEV site | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Recombinant DNA reagent | Skd3NBD in pMAL C2 with TEV site | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | ClpA (Escherichia coli) | This study | UniProtKB:P0ABH9 | Full description can be found in Materials and methods: Purification of Skd3 |
| Sequence-based reagent | ClpB (Escherichia coli) | This study | UniProtKB:P63284 | Full description can be found in Materials and methods: Purification of Skd3 |
| Sequence-based reagent | ClpC (Staphylococcus aureus) | This study | UniProtKB:Q2G0P5 | Full description can be found in Materials and methods: Purification of Skd3 |
| Sequence-based reagent | Hsp104 (Saccharomyces cerevisiae) | This study | UniProtKB:P31539 | Full description can be found in Materials and methods: Purification of Skd3 |
| Sequence-based reagent | Hsp78 (Saccharomyces cerevisiae) | This study | UniProtKB:P33416 | Full description can be found in Materials and methods: Purification of Skd3 |
| Sequence-based reagent | HAX1 (Homo sapiens) | This study | UniProtKB:O00165 | Full description can be found in Materials and methods: Purification of Skd3 |
| Sequence-based reagent | Skd3 (Ailuropoda melanoleuca) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Anolis carolinensis) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Bos taurus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Callithrix jacchus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Callorhinus ursinus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Canis lupus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Capra hircus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Carlito syrichta) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Cebus capucinus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Ceratotherium simum) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Cercocebus atys) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Chlorocebus sabaeus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Colobus angolensis) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Danio rerio) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Equus asinus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Equus caballus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Equus przewalskii) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Felis catus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Geospiza fortis) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Gorilla gorilla) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Gulo gulo) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Grammomys surdaster) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Homo sapiens) | This study | UniProtKB:Q9H078 | Full description can be found in Materials and methods: Purification of Skd3 |
| Sequence-based reagent | Skd3 (Macaca fascicularis) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Macaca mulatta) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Macaca nemestrina) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Mandrillus leucophaeus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Microcebus murinus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Microtus ochrogaster) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Monosigia brevicollis) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Mus musculus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Mustela putorius) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Nomascus leucogenys) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Nothobranchius rachovii) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Odobenus rosmarus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Orycteropus afer) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Pan paniscus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Pan troglodyte) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Panthera tigris) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Papio anubis) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent |
Skd3 (Piliocolobus tephrosceles) |
This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Pongo abelii) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Propithecus coquereli) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Puma concolor) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Rattus norvegicus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Rhinopithecus bieti) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Rhinopithecus roxellana) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Rousettus aegyptiacus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Sus scrofa) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Theropithecus gelada) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Trachymyrmex septentrionalis) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Trichinella papuae) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Ursus arctos) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Ursus maritimus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Xenopus laevis) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Sequence-based reagent | Skd3 (Zalophus californianus) | This study | Full description can be found in Materials and methods: Purification of Skd3 | |
| Software, algorithm | BOXSHADE | Hofmann and Baron, 1996 | ||
| Software, algorithm | Clusal Omega | Madeira et al., 2019 | ||
| Software, algorithm | EXPASY ProtParam | Kyte and Doolittle, 1982; Wilkins et al., 1999 | ||
| Software, algorithm | FigTree | Rambaut, 2012 | ||
| Software, algorithm | Gene Ontology (GO) | Ashburner et al., 2000; Mi et al., 2019; The Gene Ontology Consortium, 2019 | ||
| Software, algorithm | IUPRED | Mészáros et al., 2018; Mészáros et al., 2009 | ||
| Software, algorithm | PhyloPic | http://phylopic.org/ | ||
| Software, algorithm | Prism 8 | GraphPad | ||
| Software, algorithm | WebLogo |
https://weblogo.
berkeley.edu/logo.cgi |