Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference |
Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Escherichia coli) | ER2566 | NEB | 1312 | Chemically competent cells |
| Gene (Escherichia coli) | clpX | E. coli (strain K12) EXPASY | UniProtKB- P0A6H1 | |
| Gene (Escherichia coli) | clpP | E. coli (strain K12) EXPASY | UniProtKB- P0A6G7 | |
| Recombinant DNA reagent | pT7 ClpX (plasmid) | Kim et al., 2000 | N-terminally His6-tagged ClpX for overexpression | |
| Recombinant DNA reagent | pT7 ClpXΔN(plasmid) | Martin et al., 2005 | N-terminally His6-tagged ClpXΔN(residues 62–424) for overexpression | |
| Recombinant DNA reagent | pT7-ClpXΔN-T199A (plasmid) | This paper, Material and methods | ClpXΔN (residues 62–424) T199A mutant, can be obtained from the Sauer lab | |
| Recombinant DNA reagent | pT7-ClpXΔN-T199S (plasmid) | This paper, Material and methods | ClpXΔN (residues 62–424) T199S mutant, can be obtained from the Sauer lab | |
| Recombinant DNA reagent | pT7-ClpXΔN-T199V (plasmid) | This paper, Material and methods | ClpXΔN (residues 62–424) T199V mutant, can be obtained from the Sauer lab | |
| Recombinant DNA reagent | pT7-ClpXΔN-V202A (plasmid) | This paper, Material and methods | ClpXΔN (residues 62–424) V202A mutant, can be obtained from the Sauer lab | |
| Recombinant DNA reagent | pT7-ClpXΔN-H230A (plasmid) | This paper, Material and methods | ClpXΔN (residues 62–424) H230A mutant, can be obtained from the Sauer lab | |
| Recombinant DNA reagent | PACYC-ClpXΔN6-TEV-cHis6 (plasmid) | Martin et al., 2005 | ClpX expression, can be obtained from the Sauer lab | |
| Recombinant DNA reagent | pT7 ClpP (plasmid) | Kim et al., 2000 | C-terminally His6-tagged ClpP for overexpression | |
| Recombinant DNA reagent | pT7-GFP-ssrA (plasmid) |
Kim et al., 2000 | Expresses fluorescent substrate for degradation assays, can be obtained from the Sauer lab | |
| Recombinant DNA reagent | pT7 GFP LAA (plasmid) | This paper | N-terminally His6-tagged GFP (1-229) substrates with a LAA C-terminal tail, for overexpression. | |
| Recombinant DNA reagent | pT7 GFP YALAA (plasmid) | This paper | N-terminally His6-tagged GFP (1-229) substrates with a YALAA C-terminal tail, for overexpression. | |
| Recombinant DNA reagent | pT7 GFP ENYALAA (plasmid) | This paper | N-terminally His6-tagged GFP (1-229) substrates with a ENYALAA C-terminal tail, for overexpression. | |
| Recombinant DNA reagent | pT7 GFP NDENYALAA (plasmid) | This paper | N-terminally His6-tagged GFP (1-229) substrates with a NDENYALAA C-terminal tail, for overexpression. | |
| Recombinant DNA reagent | pT7 GFP AANDENYALAA (plasmid) | This paper | N-terminally His6-tagged GFP (1-229) substrates with a AANDENYALAA C-terminal tail, for overexpression. | |
| Peptide, recombinant protein | ABZ-FAPHMALVPYNO2GYGGKKLAANDENYALAA-COO- | This paper | Fluorescent peptide, for degradation assays | |
| Peptide, recombinant protein | ABZ-FAPHMALVPYNO2GYGGKKLAANDENYALGA-COO- | This paper | Fluorescent peptide, for degradation assays | |
| Peptide, recombinant protein | ABZ-FAPHMALVPYNO2GYGGKKLAANDENYALIA-COO- | This paper | Fluorescent peptide, for degradation assays | |
| Peptide, recombinant protein | ABZ-FAPHMALVPYNO2GYGGKKLAANDENYALFA-COO- | This paper | Fluorescent peptide, for degradation assays | |
| Peptide, recombinant protein | ABZ-FAPHMALVPYNO2GYGGKKLAANDENYALDA-COO- | This paper | Fluorescent peptide, for degradation assays | |
| Peptide, recombinant protein | ABZ-FAPHMALVPYNO2GYGGKKLAANDENYALKA-COO- | This paper | Fluorescent peptide, for degradation assays | |
| Peptide, recombinant protein | ABZ-FAPHMALVPYNO2GYGGKKLAANDENYALAG-COO- | This paper | Fluorescent peptide, for degradation assays | |
| Peptide, recombinant protein | ABZ-FAPHMALVPYNO2GYGGKKLAANDENYALAI-COO- | This paper | Fluorescent peptide, for degradation assays | |
| Peptide, recombinant protein | ABZ-FAPHMALVPYNO2GYGGKKLAANDENYALAF-COO- | This paper | Fluorescent peptide, for degradation assays | |
| Peptide, recombinant protein | ABZ-FAPHMALVPYNO2GYGGKKLAANDENYALAD-COO- | This paper | Fluorescent peptide, for degradation assays | |
| Peptide, recombinant protein | ABZ-FAPHMALVPYNO2GYGGKKLAANDENYALAK-COO- | This paper | Fluorescent peptide, for degradation assays | |
| Peptide, recombinant protein | ABZ-FAPHMALVPYNO2GYGGKKLAANDENYALAA-CONH2 | This paper | Fluorescent peptide, for degradation assays | |
| Software, algorithm | Relion | Zivanov et al., 2018 | RRID:SCR_016274 | EM reconstruction software |
| Software, algorithm | UCSF Chimera | Pettersen et al., 2004 | RRID:SCR_004097 | Molecularvisualizationsoftware |
| Software, algorithm | UCSF ChimeraX | Goddard et al., 2018 | RRID:SCR_015872 | Molecularvisualizationsoftware |
| Software, algorithm | Phenix | Adams et al., 2010 | RRID:SCR_014224 | Structure refinement software |
| Software, algorithm | MolProbity | Williams et al., 2018 | RRID:SCR_014226 | Protein modelevaluationsoftware |
| Software, algorithm | PyMOL | Schrödinger, LLC. | RRID:SCR_000305 | Molecularvisualizationsoftware |
| Software, algorithm | Coot | Emsley and Cowtan, 2004 | RRID:SCR_014222 | Protein modelbuildingsoftware |
| Software, algorithm | Ctffind | Rohou and Grigorieff, 2015 | RRID:SCR_016732 | EM image analysis software |
| Software, algorithm | PISA | 'Protein interfaces, surfaces and assemblies' service PISA at the European Bioinformatics Institute (http://www.ebi.ac.uk/pdbe/prot_int/pistart.html) |
RRID:SCR_015749 | Protein modelanalysis software |