| Antibodies |
| Rabbit polyclonal Anti-ubiquitin |
Dako |
Cat#z0458; RPID: AB_2315524 |
| Rabbit monoclonal K11 Ubiquitin linkage specific, clone 2A3/2E6 |
Merck-Millipore |
Cat# MABS107-I; RRID:AB_2713901 |
| Rabbit monoclonal K48 Ubiquitin linkage specific, clone Apu2 |
Merck-Millipore |
Cat# 05-1307; RRID:AB_1587578 |
| Rabbit monoclonal K63 Ubiquitin linkage specific, clone Apu3 |
Merck-Millipore |
Cat# 05-1308; RRID:AB_1587580 |
| IgG goat anti-rabbit (H L)-HRP conjugate |
BioRad |
Cat#170-6515; RPID: AB_11125142 |
| IgG H&L Goat anti-rabbit (Cy5®) preadsorbed |
Abcam |
Cat#ab97077; RPID: AB_10679461 |
| Mouse anti-HA monoclonal unconjugated (clone 12CA5) |
Roche |
Cat# 11583816001; RRID: AB_514505 |
| Bacterial and Virus Strains |
| BL-21(DE3) Rosetta™ Chemically Competent E. coli
|
Novagen |
Cat# 71397 |
| M15 Chemically Competent Cells |
Qiagen |
N/A |
| MAX Efficiency™ DH5α™ Chemically Competent Cells |
ThermoFisher |
Cat#18258012 |
| Biological Samples |
| Human Proteasomes - erythrocyte isolated |
BioMol/Enzo Life Sciences |
Cat# BML-PW9310-0050 |
| Yeast (S. cerevisiae) proteasomes |
Mansour et al., 2015 |
N/A |
| ER-derived microsomes |
Nakatsukasa et al., 2008 |
N/A |
| Chemicals, Peptides, and Recombinant Proteins |
| 2-mercaptoethanol 99% |
Sigma-Aldrich |
Cat#M3148 |
| Dithiothreitol (DTT) |
Gold Bio |
Cat#DTT25 |
| Isopropyl-β-D-1-thiogalactoside (IPTG) |
Gold Bio |
Cat#I2481C50 |
| Complete protease inhibitor cocktail |
Roche |
Cat#11836145001 |
| Potassium Phosphate dihydrate KH2PO4
|
Merck |
Cat#529568 |
| Potassium Phosphate dibasic K2HPO4
|
Merck |
Cat#105104 |
| Sodium Phosphate dihydrate NaH2PO4
|
Merck |
Cat#567545 |
| Sodium Phosphate dibasic Na2HPO4
|
Merck |
Cat#567550 |
| Ampicillin sodium salt |
Sigma |
Cat#A9518 |
| Kanamycin |
Sigma |
Cat#K4000 |
| Chloroamphenicol |
Sigma |
Cat#C0378 |
| KOD Hot Start Master Mix |
Novagen |
Cat#71842 |
| Phenylmethanesulfonyl fluoride (PMSF) |
Sigma-Aldrich |
Cat#P7626 |
| IGEPAL CA-630 |
Sigma-Aldrich |
Cat#18896 |
| Adenosine 5′-triphosphate, disodium, trihydrate (ATP) |
Fisher Scientific |
Cat#10326943 |
| Ammonium Chloride (15N, 99%) |
Cambridge Isotope Laboratories, Inc |
Cat#NLM-467 |
| D-Glucose (U-13C6, 99%) |
Cambridge Isotope Laboratories, Inc |
CLM-1396-5 |
| Albumin, from Bovine Serum |
Sigma-Aldrich |
Cat#A3294 |
| Coomassie R-250 Brilliant Blue |
ThermoFisher |
Cat#20278 |
| Tris(2-carboxyethyl)phosphine-HCl (TCEP-HCl) |
Gold Bio |
Cat# TCEP25 |
| MG132 |
Calbiochem Merck Millipore |
Cat#474790 |
| 1-oxyl-2,2,5,5-tetramethyl-3-pyrroline-3-methyl methanesulfonate (MTSL) |
Toronto Research Chemicals |
Cat#O875000 |
| Wheat Germ Agglutinin, Texas Red® conjugate |
Life Technologies |
Cat#W7024 |
| Oregon Green® 488 maleimide |
ThermoFisher |
Cat#O6034 |
| I125-Ubiquitin |
This work |
|
| Ub4pep∼Oregon Green® conjugate |
This work |
|
| Ubistatin B (ubiB) |
Verma et al., 2004 |
N/A |
| Ubistatin compound 1 |
This work |
N/A |
| Ubistatin compound 2 |
This work |
N/A |
| Ubistatin compound 3 |
This work |
N/A |
| Ubistatin compound 4 |
This work |
N/A |
| Ubistatin compound 5 |
This work |
N/A |
| Ubistatin compound 6 |
This work |
N/A |
| Ubistatin compound 7 |
This work |
N/A |
| Ubistatin compound 8 |
This work |
N/A |
| Ubistatin compound 9 / Hemi-ubistatin B (h-ubiB) |
This work |
N/A |
| Hemi-Ubistatin compound 10 |
This work |
N/A |
| Related ubistatin compound 11 |
This work |
N/A |
| 8-Anilino-1-naphthalenesulfonic acid (ANS) |
Sigma |
Cat#A1028-5G |
|
15N-labeled (distal) dimeric Ub (K48-Ub2) |
This work |
N/A |
|
15N-labeled (distal) dimeric Ub (K63-Ub2) |
This work |
N/A |
|
15N-labeled monomeric Ub |
This work |
N/A |
|
13C/15N-labeled monomeric Ub |
This work |
N/A |
|
15N-labeled monomeric UbR42A
|
This work |
N/A |
|
15N-labeled monomeric UbR42E
|
This work |
N/A |
|
15N-labeled monomeric UbR72A
|
This work |
N/A |
|
15N-labeled monomeric UbR72E
|
This work |
N/A |
|
15N-labeled monomeric UbR42E,R72E
|
This work |
N/A |
|
15N-labeled monomeric UbR74A
|
This work |
N/A |
|
15N-labeled monomeric UbR74E
|
This work |
N/A |
|
15N-labeled monomeric UbK63D
|
This work |
N/A |
|
15N-labeled monomeric Ub72 (∆73-76) |
This work |
N/A |
|
15N-labeled monomeric UbT12C
|
This work |
N/A |
|
15N-labeled monomeric UbI36C
|
This work |
N/A |
|
15N-labeled monomeric UbK48C
|
This work |
N/A |
|
15N-labeled monomeric UbK63C
|
This work |
N/A |
|
15N-labeled RUB1 |
Singh et al., 2012 |
N/A |
|
15N--labeled UBA of UBQLN1 |
This work |
N/A |
| K11-linked dimeric Ub (K11-Ub2) |
This work |
N/A |
| K11-linked >hexameric Ub (K11-Ub6+) |
This work |
N/A |
| K48-linked dimeric Ub (K48-Ub2) |
This work |
N/A |
| K63-linked dimeric Ub (K63-Ub2) |
This work |
N/A |
| 6xHis-Ubp6 full length |
This work |
N/A |
| GST-Cezanne OTUD7B (OTU domain) |
This work |
N/A |
| 6xHis-OTUB1 (OTU domain) |
This work |
N/A |
| GST-AMSH (JAMM/MPN+ domain) |
This work |
N/A |
| UbcH5B-Ubn
|
This work |
N/A |
| Experimental Models: Cell Lines |
| HeLa |
ATCC |
ATCC® CCL-2™ |
| RCC4 |
Gift from Allan Weissman (NCI) |
N/A |
| Recombinant DNA |
| pJexpress401 Ub4pep |
This work |
N/A |
| pET3a untagged Human wild-type Ubiquitin |
Varadan et al., 2002 |
N/A |
| pET3a untagged UbR42A
|
This work |
N/A |
| pET3a untagged UbR42E
|
This work |
N/A |
| pET3a untagged UbR72A
|
This work |
N/A |
| pET3a untagged UbR72E
|
This work |
N/A |
| pET3a untagged UbR42E/R72E
|
This work |
N/A |
| pET3a untagged UbR74A
|
This work |
N/A |
| pET3a untagged UbR74E
|
This work |
N/A |
| pET3a untagged UbK63D
|
This work |
N/A |
| pET3a untagged Ub72
|
This work |
N/A |
| pET3a untagged UbT12C
|
This work |
N/A |
| pET3a untagged UbI36C
|
This work |
N/A |
| pET3a untagged UbK48C
|
This work |
N/A |
| pET3a untagged UbK63C
|
This work |
N/A |
| pTXB1-RUB1 |
Singh et al., 2012 |
N/A |
| pGEX2T-1 UBQLN1 UBA domain |
Raasi et al., 2005 |
N/A |
| pQE30 Ubp6 full length |
Mansour et al., 2015 |
N/A |
| pOPINK Cezanne/OTUD7B 53-446 (OTU domain) |
(Mevissen et al., 2013) |
Addgene:61581 |
| pProEX-OTUB1 (OTU domain) |
(Wang et al., 2009) |
Addgene:26959 |
| AMSH |
Fushman Lab |
N/A |
| pET3a human UbcH5B |
Mansour et al., 2015 |
N/A |
| pSM1152 (2μ URA3 PPGKCFTR∷HA) |
Nakatsukasa et al., 2008 |
N/A |
| Software and Algorithms |
| ImageGauge version 3.45 |
Fuji Life Sciences |
www.fujifilm.com |
| Marvinsketch |
ChemAxon |
http://www.chemaxon.com |
| ORCA package |
Max-Planck Institut für Chemische Energiekonversion |
https://orcaforum.cec.mpg.de/ |
| PRODRG server |
GlycoBioChem Ltd. |
http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg |
| LIGPLOT program |
EMBL-EBI |
https://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/ |
| Vinci software |
Vinci Inc. |
http://www.iss.com/fluorescence/software/vinci.html |
| Zen Lite |
Carl Zeiss |
www.zeiss.com |
| Fiji |
LOCI - University of Wisconsin-Madison. |
https://fiji.sc |
| Bruker Topspin version 3.5 |
Bruker Inc. |
www.bruker.com |
| Computer aided resonance assignment (CARA) |
Wüthrich lab, ETH |
Cara.nmr.ch |
| SPARKY 3 |
Goddard and Kneller, UCSF |
https://www.cgl.ucsf.edu/home/sparky/ |
| HADDOCK v2.1 |
Bonvin Lab, University of Utrecht |
haddock.science.uu.nl/ |
| SASSIE |
NCNR, NIST |
https://sassie-web.chem.utk.edu/sassie2/ |
| PyMOL |
Schrödinger, LLC |
http://www.pymol.org |
| KdFit, Matlab program for analysis of titration data |
Fushman Lab |
http://gandalf.umd.edu/FushmanLab/pdsw |
| SLfit, Matlab program for analysis of spin-labeling data |
Fushman Lab |
http://gandalf.umd.edu/FushmanLab/pdsw |
| Other |
| 5 mL GST Trap |
GE Life Sciences |
Cat#17513001 |
| 5 mL His Trap |
GE Life Sciences |
Cat#17-5248-01 |
| 5 mL SP HP |
GE Life Sciences |
Cat#17-5054-01 |
| 16/60 Superdex 75 |
GE Life Sciences |
Cat#28989333 |
| Protein A Sepharose CL4B |
GE Life Sciences |
Cat#17-0780-01 |
| 4.6 × 30 mm XBridge C18 3.5 μm column |
Waters |
N/A |
