KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse Monoclonal Anti-HA | AbLab | Cat# 12CA5 |
| Rabbit Polyclonal Anti-Pgk1 | Acris | Cat# AP21371AF-N |
| IRDye® 800CW Goat Anti-Mouse IgG | LI-COR | Cat# 926-32210 |
| IRDye® 800CW Goat Anti-Rabbit IgG | LI-COR | Cat# 926-32211 |
| Bacterial and virus strains | ||
| NEB5α Competent E. coli | NEB | Cat# C2987I |
| Chemicals, peptides, and recombinant proteins | ||
| Difco™ Yeast Nitrogen Base without Amino Acids | BD Life Sciences | Cat# 291940 |
| 13C6 Arg-6 | Silantes | Cat# 201204102 |
| 13C6 15N4 Arg-10 | Silantes | Cat# 201604102 |
| D4 Lys-4 | Silantes | Cat# 211104113 |
| 13C6 15N2 Lys-8 | Silantes | Cat# 211604102 |
| IGEPAL® CA-630 (NP-40) | Sigma-Aldrich | Cat# I3021-100ML |
| Phenylmethylsulfonyl fluoride (PMSF) | Roche | Cat# 1359061 |
| cOmplete™, EDTA-free Protease Inhibitor Cocktail (PIC) | Roche | Cat# 5056489001 |
| Proteinase K | SIGMA | Cat# P2308-100MG |
| SigmaUltra Iodoacetamide | Sigma-Aldrich | Cat# I1149 |
| Tris-(2-carboxyethyl)phosphine (TCEP) | Gold Biotechnology | Cat# TCEP25 |
| Sequencing Grade Modified Trypsin, Frozen | Promega | Cat# V5113 |
| Sera-Mag™ SpeedBead Carboxylate-Modified [E7] Magnetic Particles | GE Healthcare | Cat# 45152105050250 |
| Sera-Mag™ SpeedBead Carboxylate-Modified [E3] Magnetic Particles | GE Healthcare | Cat# 65152105050250 |
| LoFlo Medium | Formedium | Cat# CYN6502 |
| Critical commercial assays | ||
| GeneJET Genomic DNA Purification Kit | Thermo Scientific | Cat# K0722 |
| GeneJET Plasmid Miniprep Kit | Thermo Scientific | Cat# K0502 |
| GenCatch™ PCR Cleanup Kit | Epoch Life Science | Cat# 2360250 |
| Pierce™ BCA Protein Assay Kit | Thermo Scientific | Cat# 23225 |
| Gibson Assembly Master Mix | NEB | Cat# E2611L |
| Deposited data | ||
| Mass spectrometry results of pellet and total cell lysate fractions for Experiments 1-3 | This paper, PRoteomics IDEntification (PRIDE) repository | PXD024336 |
| Mass spectrometry results of supernatant fractions of Experiment 1 and the LiP experiment | This paper, PRoteomics IDEntification (PRIDE) repository | PXD028934 |
| Codes used for the bulk of the feature analysis in Figures 5, 6 and 7 | This paper | https://doi.org/10.5281/zenodo.6640632 |
| Codes used for the number of pfam domains (Figure S5A), contact order (Figure 6B) and SASA analysis (Figure 7E) | This paper | https://doi.org/10.5281/zenodo.6639064 |
| Code and data set for the analysis of native lasso-like self-entanglements (Figures 6C and 7F) | This paper | https://doi.org/10.5281/zenodo.6642237 |
| Experimental models: Organisms/strains | ||
| BY4741 strains (MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0) | Hieter lab | YTM408 |
| SILAC strain (MATa, his3Δ1, leu2Δ0, ura3Δ0, MET15, arg4Δ::KanMX6, lys2Δ0) | Measday lab | YTM1173 |
| Oligonucleotides | ||
| Oligonucleotides, See Table S5 | This paper | n/a |
| Recombinant DNA | ||
| pRS316-CUP1p-mCherry-sfGFP-ADH1t | This paper | BPM1455 |
| pRS316-CUP1p-RPL12B-mCherry-sfGFP-ADH1t | This paper | BPM1761 |
| pRS316-CUP1p-OLA1-mCherry-sfGFP-ADH1t | This paper | BPM1762 |
| pRS426-GAL1p-3HA-CYC1t | This paper | BPM1809 |
| pRS426-GAL1p-TPI1-3HA-CYC1t | This paper | BPM1819 |
| pRS426-GAL1p-HRI1-3HA-CYC1t | This paper | BPM1820 |
| pRS426-GAL1p-RPL12A-3HA-CYC1t | This paper | BPM1822 |
| pRS426-GAL1p-ARG1-3HA-CYC1t | This paper | BPM1823 |
| Software and algorithms | ||
| Bruker Compass HyStar 5.0 SR1 | Bruker Daltonics | Ver. 5.0.37.0 |
| MaxQuant | Computational Systems Biochemistry under Prof. Jürgen Cox | 1.6.14 |
| Zen 3.0 | Zeiss | n/a |
| Illustrator | Adobe Creative | n/a |
| Image Studio | LI-COR | Ver. 2.1 |