Key Resources Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and Virus Strains | ||
| Escherichia coli BL21(DE3) | Invitrogen | C600003 |
| Escherichia coli BL21(DE3)pLysS | Invitrogen | C606003 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| D2O | Sigma-Aldrich | 191701 |
| 13C glucose | Cambridge Isotope Laboratories, Inc. | CLM-1396–5 |
| PreScission protease | GE Healthcare Life Sciences | GE27-0843-01 |
| protease inhibitor cocktail | Roche | 04693159001 |
| inorganic pyrophosphatase | Sigma-Aldrich | I1643–100UN |
| creatine kinase | Sigma-Aldrich | C3755–1KU |
| ATP | Sigma-Aldrich | A2383–5G |
| E1 | Boston Biochem, Inc. | E-306 |
| Isopropyl- β-D-thiogalactoside | UBPBio | P1010–10 |
| Glutathione S-sepharose 4B | GE Healthcare Life Sciences | 17-0756-05 |
| SP-Sepharose | GE Healthcare Life Sciences | 17-0729-10 |
| Talon Metal Affinity resin | Clontech Laboratories, Inc. | 635502 |
| E2–25K | This paper | N/A |
| hRpn13 Pru (1–150) | This paper | N/A |
| hRpn2 (940–953) | This paper | N/A |
| Ub-D77 | This paper | N/A |
| Ub-K48R | This paper | N/A |
| K48-diubiquitin | This paper | N/A |
| Deposited Data | ||
| Crystal structure of K48-tetraubiquitin | (Phillips et al., 2001) | PDB: 1F9J |
| Crystal structure of K48-tetraubiquitin | (Eddins et al., 2007) | PDB: 2O6V |
| Crystal structure of cyclic K48-tetraubiquitin | (Satoh et al., 2010) | PDB: 3ALB |
| Crystal structure of K48-tetraubiquitin | (Cook et al., 1994) | PDB: 1TBE |
| Crystal structure of Ube2K with K48-diubiquitin | (Lee et al., 2018) | PDB: 6IF1 |
| NMR structure of gp78 E3 ligase CUE domain with K48-diubiquitin | (Liu et al., 2012) | PDB: 2LVP, 2LVQ |
| Crystal structure of MINDY-1 tMIU with K48-diubiquitin | (Kristariyanto et al., 2017) | PDB: 5MN9 |
| NMR structure of Rpn1 with K48-diubiquitin | (Shi et al., 2016) | PDB: 2N3V, 2N3W |
| NMR structure of hRpn10 with K48-diubiquitin | (Zhang et al., 2009) | PDB: 2KDE, 2KDF |
| NMR solution structure of monoubiquitin | (Cornilescu et al., 1998) | PDB: 1D3Z |
| Crystal structure of monoubiquitin | (Vijay-Kumar et al., 1987) | PDB: 1UBQ |
| Crystal structure of K48-diubiquitin in the “closed” conformation | (Cook et al., 1992) | PDB: 1AAR |
| Crystal structure of K48-diubiquitin in the “open” conformation | (Hirano et al., 2011) | PDB: 3AUL |
| NMR solution structure of hRpn13 Pru:hRpn2 | (Lu et al., 2017) | PDB: 6CO4 |
| Crystal structure of hRpn13 Pru:hRpn2:monoubiquitin | (VanderLinden et al., 2017) | PDB: 5V1Y |
| NMR solution structure of hRpn13 Pru:K48-diubiquitin | (Liu et al., 2019) | PDB: 5YMY |
| Chemical shift data for Ternary-P and Ternary-D | This paper | BMRB: 28042 |
| NMR structure of Ternary-P | This paper | PDB: 6UYI |
| NMR structure of Ternary-D | This paper | PDB: 6UYJ |
| Software and Algorithms | ||
| XPLOR-NIH | (Schwieters et al., 2003) | http://nmr.cit.nih.gov/xplor-nih/ |
| XEASY | (Bartels et al., 1995) | N/A |
| NMRPipe | (Delaglio et al., 1995) | https://www.ibbr.umd.edu/nmrpipe/install.html |
| PROCHECK-NMR | (Laskowski et al., 1996) | https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/ |
| PyMOL | N/A | http://www.pymol.org |
| MOLMOL | (Koradi et al., 1996) | https://sourceforge.net/projects/molmol/ |