KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Monoclonal Anti-Green Fluorescent Protein (GFP) antibody, clone GFP-20 | Sigma | Cat#6539 |
| Bacterial and virus strains | ||
| Sf9 Insect Cells | Sigma-Aldrich | Cat#71104–3 |
| Bac-to-Bac™ Baculovirus Expression System | ThermoFisher | Cat#10359016 |
| Escherichia coli BL21 Rosetta™ (DE3) | Merck | Cat#70954 |
| Chemicals, peptides, and recombinant proteins | ||
| β-Nicotinamide adenine dinucleotide, reduced disodium salt (NADH) |
Sigma-Aldrich | Cat#N7410 |
| Adenosine 5’-triphosphate disodium salt hydrate | Sigma-Aldrich | Cat#A6419 |
| Adenylyl-imidodiphosphate (AMPPNP) | Roche | Cat#10102547001 |
| Antibiotic-antimyocotic | ThermoFisher | Cat#5240062 |
| Dimethylsulfoxide (DMSO) | Sigma-Aldrich | Cat#276855 |
| D-Lactic Dehydrogenase (LDH) | Sigma-Aldrich | Cat#L3888 |
| Phospho(enol)pyruvic acid monopotassium salt (PEP) | Sigma-Aldrich | Cat#P7127 |
| Phenylmethylsulfonyl fluoride (PMSF) | Sigma-Aldrich | Cat#P7626 |
| Pyruvate Kinase from rabbit muscle (PK) | Sigma-Aldrich | Cat#P9136 |
| Roche cOmplete, EDTA-free Protease Inhibitor | Sigma-Aldrich | Cat#11873580001 |
| Tris(2-carboxyethyl)phosphine HCl (TCEP) | Sigma-Aldrich | Cat# C4706 |
| Triton™ X-100 | Sigma-Aldrich | Cat#X100 |
| IgG Sepharose® 6 Fast Flow | Cytiva | Cat#GE17–0969-01 |
| Sodium acetate trihydrate | Sigma-Aldrich | Cat#71188 |
| Sf-900™ II SFM | ThermoFisher | Cat#10902096 |
| Fetal Bovine Serum | Sigma-Aldrich | Cat# F4135 |
| Taxol | Sigma-Aldrich | Cat#T7191 |
| Glucose Oxidase from Aspergillus niger | Sigma-Aldrich | Cat#G2133 |
| Catalase from bovine liver | Sigma-Aldrich | Cat#C40 |
| Polyethylene glycol 3350 (PEG-3350) | Sigma-Aldrich | Cat#202444 |
| Dithiothreitol (DTT) | Gold Biotechnology | Cat#DTT25 |
| ATP, [γ-32P] | PerkinElmer | BLU002Z250UC |
| TLC PEI Cellulose F | Millipore Sigma | Cat#1055790001 |
| Hepes, ≥99.5% (titration) | Sigma-Aldrich | Cat#H3375 |
| Magnesium acetate tetrahydrate | Sigma-Aldrich | Cat#M5661 |
| Critical commercial assays | ||
| Monolith NT Protein Labeling Kit RED-NHS | Nanotemper | SKU:MO-L001 |
| Deposited data | ||
| Dynein motor domain – ADP complex (template for molecular replacement) | (Schmidt et al., 2012) | PDB: 4AI6 |
| Dynein motor domain – ATP complex | (Schmidt et al., 2012) | PDB: 4AKG |
| Motor domain from human cytoplasmic dynein-1 | (Zhang et al., 2017) | PDB: 5NUG |
| Crystal structure of the dynein motor domain in the AMPPNP-bound state | (Bhabha et al., 2014) | PDB: 4W8F |
| Yeast dynein motor domain in the presence of a pyrazolo-pyrimidinone-based compound, Model 1 | This paper | PDB: 7MI6 |
| Yeast dynein motor domain in the presence of a pyrazolo-pyrimidinone-based compound, Map 1 | This paper | EMD-23841 |
| Signal subtracted reconstruction of the AAA1 domain of dynein in the presence of a pyrazolo-pyrimidinone-based compound, Map 2 | This paper | EMD-23844 |
| Signal subtracted reconstruction of the AAA1 domain of dynein in the presence of a pyrazolo-pyrimidinone-based compound, Map 3 | This paper | EMD-23846 |
| Signal subtracted reconstruction of AAA2, AAA3, and AAA4 domains of dynein in the presence of a pyrazolo-pyrimidinone-based compound, Model 4 | This paper | PDB: 7MI3 |
| Signal subtracted reconstruction of AAA2, AAA3, and AAA4 domains of dynein in the presence of a pyrazolo-pyrimidinone-based compound, Map 4 | This paper | EMD-23838 |
| Signal subtracted reconstruction of AAA5 and AAA5 domains of dynein in the presence of a pyrazolo-pyrimidinone-based compound, Model 5 | This paper | PDB: 7MI8 |
| Signal subtracted reconstruction of AAA5 and AAA5 domains of dynein in the presence of a pyrazolo-pyrimidinone-based compound, Map 5 | This paper | EMD-23842 |
| X-ray structure of yeast dynein motor domain in the presence of a pyrazolo-pyrimidinone-based compound | This paper | PDB: 7MI1 |
| Experimental models: organisms/strains | ||
| GFP-Sc-Dyn (VY137): PDyn:pGal:ZZ:Tev:GFP:HA:D6 MATa; his3–11,15; ura3–1; leu2–3,112; ade2–1; trp1–1; pep4Δ:HIS5; prb1Δ | (Reck-Peterson et al., 2006) | N/A |
| Sc-Dynlyso (VY1027): PDyn:PGal:ZZ:Tev:D4.6_CC10 MATa; his3–11,5; PEP4::HIS5 PRB1D; trp1–1; leu2–3,112; ade2–1; ura3–1 | (Bhabha et al., 2014) | N/A |
| Sc-DynlysoMut (VY972): PDyn:PGal:ZZ:Tev:D4.6_AAA1E/Q_CC10 MATa; his3–11,5; PEP4::HIS5 PRB1D; trp1–1; leu2–3,112; Ade; ura3–1 | (Bhabha et al., 2014) | N/A |
| Sc-DynGST (VY208): DpDyn-pGAL-ZZ-TEV-GFP-3XHA-GST-D6-DYN1-gsDHA:Kan | (Reck-Peterson et al., 2006) | N/A |
| Recombinant DNA | ||
| Plasmid: Hs-Dynein 1 | (Steinman et al., 2017) | N/A |
| pQE9-His-p97 (M. musculus VCP/p97) | (Meyer et al., 2000) | Addgene #14666 |
| pDEST15-FIGL1 (H. sapiens FIGL1) | (Cupido et al., 2019) | N/A |
| pMAL-c5x-p60 (X. laevis katanin p60) | (Loughlin et al., 2011) | N/A |
| pDEST15-Dm-spastin (D. melanogaster spastin) | (Roll-Mecak and Vale, 2008) | N/A |
| Software and algorithms | ||
| MATLAB R018b | MathWorks | https://www.mathworks.com/ |
| FIESTA | (Ruhnow et al., 2011) | https://fusionforge.zih.tu-dresden.de/plugins/mediawiki/wiki/fiesta/index.php/FIESTA |
| PHENIX 1.13_2998 | PHENIX | https://www.phenix-online.org/ |
| XDS 20180319 | XDS | https://xds.mr.mpg.de/ |
| Schrodinger Maestro, release 2019–4 | Schrodinger LLC | https://www.schrodinger.com |
| UCSF Chimera package version 1.14 | UCSF | https://www.cgl.ucsf.edu/chimera/ |
| Other | ||
| Monolith premium capillary tubes | Nanotemper | SKU:MO-K022 |
| Corning 384 Well Black NBS Flat Bottom Assay Plates | Corning | Cat#3654 |