KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and virus strains | ||
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| E. coli DH5alpha competent cells | ThermoFisher | Cat# 18265017 |
| E. coli BL21(DE3) competent cells | ThermoFisher | Cat# EC0114 |
| E. coli DH10Bac competent cells | ThermoFisher | Cat# 10361012 |
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| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| Protease inhibitor | MilliporeSigma | Cat# 11873580001 |
| DyLight™ 800 Maleimide | Thermo Fisher | Cat # 46621 |
| Plasmid Mega Kit | Qiagen | Cat # 12181 |
|
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| Deposited data | ||
|
| ||
| UBR5 structure model (C1 symmetry in dimer) | This study | PDB: 8D4X |
| UBR5 structure model (C2 symmetry in dimer) | This study | PDB: 8E0Q |
| UBR5 structure model (C1 symmetry in tetramer) | This study | PDB: 8EWI |
| UBR5 structure map (C1 symmetry in dimer) | This study | EMDB: EMD-27201 |
| UBR5 structure model (C2 symmetry in dimer) | This study | EMDB: EMD-27822 |
| UBR5 structure model (C1 symmetry in tetramer) | This study | EMDB: EMD-28646 |
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| Experimental models: Cell lines | ||
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| Sf9 insect cells | Invitrogen | Cat# 11496015 |
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| Oligonucleotides | ||
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| ||
| GCGCGGAATTCATGGACTACAAGGACGACGACGACAAGATGCAGCACATCCTGAGGTGCGACTACG | Eurofins Scientific | UBR5(876-2799)_forward |
| CGAAAGCGGCCGCTTATTACACGAAACCGAAGTTCTTGGTCT | Eurofins Scientific | UBR5(876-2799)_reverse |
| CCGCGCGGCAGCCATATGTGTCAGATCTTCGTGAAAACCC | Eurofins Scientific | Cys-Ub_forward |
| GTGGTGGTGGTGCTCGAGTCAACCACCTCTCAGACGCAGG | Eurofins Scientific | Cys-Ub_reverse |
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| Recombinant DNA | ||
|
| ||
| pFastBac_UBR5 | This study | N/A |
| pET28a_Cys-ub | This study | N/A |
| pET28a-PEPCK1 | This study | N/A |
|
| ||
| Software and algorithms | ||
| cryoSPARC v3.2.0 | Punjani et al., 201774 | https://cryosparc.com/ |
| MotionCor2 | Zheng et al., 201775 | https://emcore.ucsf.edu/ucsf-software |
| Coot v0.9.4 | Emsley et al., 200476 | https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ |
| Phenix v1.20 | Adams et al., 201077 | https://phenix-online.org/documentation/reference/autobuild_gui.html |
| ChimeraX | Goddard et al.,201878 | https://www.cgl.ucsf.edu/chimerax/docs/user/index.html |
| Chimera | Pettersen et al., 200479 | http://www.cgl.ucsf.edu/chimera/ |
| DeepEMhancer | Sanchez-Garcia et al., 202180 | https://github.com/rsanchezgarc/deepEMhancer |
| AlphaFold2 | Jumper et al., 202165 | https://github.com/deepmind/alphafold |
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| Others | ||
| Quantifoil Au R2/1 | SPI Supplies | Cat# 4330G-FA |
| easiGlow glow discharger | PELCO | Model# 91000 |
| Vitrobot | Thermo Fisher | N/A |
| Superose 6 Increase10/300 GL | Sigma-Aldrich | Cat# GE29-0915-96 |