Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference |
Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Mus musculus) | RNF213 | RefSeq | HGNC:14539; RefSeq: NP_001035094.2 | |
| Strain, strain background (Escherichia coli) |
DH10EmBacY | Geneva Biotech | DH10EmBacY | Strain propagated locally from source commercial stock |
| Strain, strain background (Escherichia coli) | BL21(DE3) | Sigma-Aldrich | CMC0016; RRID:NCBITaxon_ 469008 | Strain propagated locally from source commercial stock |
| Strain, strain background (AcMNPV) |
EmBacY | Geneva Biotech | ||
| Cell line (Spodoptera frugiperda) | Sf9 | Thermo Fisher Scientific | IPLB-Sf-21-AE; RRID:CVCL_0549 | Strain propagated locally from source commercial stock |
| Cell line (Trichoplusia ni) | High Five | Thermo Fisher Scientific | BTI-TN-5B1-4; RRID:CVCL_C190 | Strain propagated locally from source commercial stock |
| Recombinant DNA reagent | pCLA00001 | This paper | addgene: 138607; RRID:Addgene_
138607 |
Bac-to-Bac compatible plasmid with wt RNF213 |
| Recombinant DNA reagent | pCLA00002 | This paper | addgene: 138608; RRID:Addgene_138608 | Bac-to-Bac compatible plasmid with MMD RNF213 |
| Recombinant DNA reagent | pCLA00003 | This paper | addgene: 138609; RRID:Addgene_138609 | Bac-to-Bac compatible plasmid with ΔRING RNF213 |
| Peptide, recombinant protein | RNF213 wild type | This paper |
NP_001035094.2: p. = |
Internal ID:Mys1b |
| Peptide, recombinant protein | RNF213 MMD | This paper |
NP_001035094.2: p.R4753K |
Internal ID:Mys18a |
| Peptide, recombinant protein | RNF213 ΔRING | This paper |
NP_001035094.2: p.3941_3999delinsGSGSG |
Internal ID:Mys_Mm_20a |
| Peptide, recombinant protein | Ub_fluor | This paper |
NP_066289.3 (1–76): p.1_2insGPLCGS |
Cysteine-labelable ubiquitin, based on DOI:10.1038/s41589-019-0426-z |
| Commercial assay or kit | DSS-H12/D12 | Creative Molecules |
001S | Cross-linking reagent used for XL-MS |
| Commercial assay or kit | DyLight 800 Maleimide | Thermo Fisher Scientific | 46621 | |
| Other | 4–20% Criterion TGX Stain-Free Protein Gel | Bio-Rad | 5678095 | For ubiqutination assay analysis |
| Other | Quantifoil R2/2 Cu 200 | Quantifoil | Quantifoil R2/2 Cu 200 | EM grid used for wt RNF213 |
| Other | UltrAuFoil R2/2 Au 200 | Quantifoil | UltrAuFoil R2/2 Au 200 | EM grid used for MMD RNF213 |
| Software, algorithm | FoldIndex | doi:10.1093/bioinformatics/bti537 | RRID:SCR_018390 | |
| Software, algorithm | CADD | doi:10.1093/nar/gky1016 | RRID:SCR_018393 | https://cadd.gs.washington.edu/snv |
| Software, algorithm | hhpred | doi:10.1093/nar/gki408 | RRID:SCR_010276 | https://toolkit.tuebingen.mpg.de/tools/hhpred |
| Software, algorithm | MUSCLE | doi:10.1093/nar/gkh340 | RRID:SCR_011812 | https://www.drive5.com/muscle/ |
| Software, algorithm | Fiji | other | RRID:SCR_002285 | https://fiji.sc/ |
| Software, algorithm | Sphire | other | RRID:SCR_018391 | http://sphire.mpg.de/ |
| Software, algorithm | gctf | doi:10.1016/j.jsb.2015.11.003 | RRID:SCR_016500 | https://www.mrc-lmb.cam.ac.uk/kzhang/ |
| Software, algorithm | ctffind | doi:10.1016/j.jsb.2015.08.008 | RRID:SCR_016732 |
https://grigoriefflab.
umassmed.edu/ |
| Software, algorithm | Relion | doi:10.7554/eLife.42166 | RRID:SCR_016274 | https://www3.mrc-lmb.cam.ac.uk/relion/ |
| Software, algorithm | cryoSPARC | doi:10.1038/nmeth.4169 | RRID:SCR_016501 | https://cryosparc.com/ |
| Software, algorithm | UCSF Chimera | doi:10.1016/j.jsb.2006.06.010 | RRID:SCR_004097 | https://www.cgl.ucsf.edu/chimera/ |
| Software, algorithm | MotionCor2 | doi:10.1038/nmeth.4193 | RRID:SCR_016499 | https://emcore.ucsf.edu/ucsf-motioncor2 |
| Software, algorithm | cryolo | doi:10.1038/s42003-019-0437-z | RRID:SCR_018392 | https://sphire.mpg.de/wiki/ |
| Software, algorithm | O | doi:10.1107/s0108767390010224 | RRID:SCR_018394 | http://xray.bmc.uu.se/~alwyn/TAJ/Home.html |
| Software, algorithm | USCF ChimeraX | doi:10.1002/pro.3235 | RRID:SCR_015872 | https://www.rbvi.ucsf.edu/chimerax/ |
| Software, algorithm | Pymol | other | RRID:SCR_000305 | https://pymol.org/2/ |
| Software, algorithm | Phenix | doi:10.1107/S2059798318006551 | RRID:SCR_014224 | https://www.phenix-online.org/ |
| Software, algorithm | xiSEARCH | doi:10.1074/mcp.M115.049296 | RRID:SCR_018395 | https://www.rappsilberlab.org/software/xisearch/ |
| Software, algorithm | MS amanda | doi:10.1021/pr500202e | RRID:SCR_018396 | http://ms.imp.ac.at/?goto=msamanda |
| Software, algorithm | IMP-apQuant | doi:10.1021/acs.jproteome.8b00113 | RRID:SCR_018397 | http://ms.imp.ac.at/index.php?action=apQuant |