IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/ lu-2021-2 in vitro In vitro fluorescence imaging fluorescence microscopy fluorescence imaging tag fluorescence tag visualisation by fluorescence tag fluorescence Lu S., Ye Q., Singh D., Cao Y., Diedrich JK., Yates JR., Villa E., Cleveland DW., Corbett KD. Virus - Publications including interactions involving viral proteins dcleveland@health.ucsd.edu, kcorbett@health.ucsd.edu Nature communications 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus lu-2021-1 in vitro In vitro light microscopy light microscopy predetermined predetermined participant predetermined Lu S., Ye Q., Singh D., Cao Y., Diedrich JK., Yates JR., Villa E., Cleveland DW., Corbett KD. Virus - Publications including interactions involving viral proteins Differential Interference Contrast (DIC) Microsopy. dcleveland@health.ucsd.edu, kcorbett@health.ucsd.edu Nature communications 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus lu-2021-3 in vitro In vitro frap fluorescence recovery after photobleaching frap tag fluorescence tag visualisation by fluorescence tag fluorescence Lu S., Ye Q., Singh D., Cao Y., Diedrich JK., Yates JR., Villa E., Cleveland DW., Corbett KD. Virus - Publications including interactions involving viral proteins dcleveland@health.ucsd.edu, kcorbett@health.ucsd.edu Nature communications 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus lu-2021-4 in vitro In vitro super-resolution microscopy Super-resolution microscopy super resolution microscopy super-resolution microscopy tag fluorescence tag visualisation by fluorescence tag fluorescence Lu S., Ye Q., Singh D., Cao Y., Diedrich JK., Yates JR., Villa E., Cleveland DW., Corbett KD. Virus - Publications including interactions involving viral proteins dcleveland@health.ucsd.edu, kcorbett@health.ucsd.edu Nature communications 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus lu-2021-5 in vitro In vitro crosslink cross-linking study crosslink sequence tag sequence tag identification sequence tag Lu S., Ye Q., Singh D., Cao Y., Diedrich JK., Yates JR., Villa E., Cleveland DW., Corbett KD. Virus - Publications including interactions involving viral proteins It has not been possible to add most Cross-links, as it is stated:- "For most cross-linked lysine pairs, (e.g., K249–K256 or K256–K374), it is impossible to determine whether the cross-link arose from intramolecular or intermolecular interactions." BS3 (bis(sulfosuccinimidyl)suberate) using BS3-d0/d4 reagents which are mass-analogs of the BS3 crosslinker. The d-zero variety (BS3-d0) possesses ordinary hydrogen atoms while the d-four variety (BS3-d4) contains four deuterium atoms that make it exactly four hydrogen mass units heavier. dcleveland@health.ucsd.edu, kcorbett@health.ucsd.edu Nature communications 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus lu-2021-7 in vitro In vitro uv-vis ultraviolet-visible spectroscopy uv-vis predetermined predetermined participant predetermined Lu S., Ye Q., Singh D., Cao Y., Diedrich JK., Yates JR., Villa E., Cleveland DW., Corbett KD. Virus - Publications including interactions involving viral proteins Turbidity measurements at 350nm. dcleveland@health.ucsd.edu, kcorbett@health.ucsd.edu Nature communications 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus lu-2021-9 human-u2-os Human U2-OS osteosarcoma cell line u2-os U2-OS osteocaroma cell line Not in CAPRI and no primary literature reference fluorescence imaging fluorescence microscopy fluorescence imaging tag fluorescence tag visualisation by fluorescence tag fluorescence Lu S., Ye Q., Singh D., Cao Y., Diedrich JK., Yates JR., Villa E., Cleveland DW., Corbett KD. Virus - Publications including interactions involving viral proteins dcleveland@health.ucsd.edu, kcorbett@health.ucsd.edu Nature communications 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus lu-2021-6 human-u2-os Human U2-OS osteosarcoma cell line u2-os U2-OS osteocaroma cell line Not in CAPRI and no primary literature reference frap fluorescence recovery after photobleaching frap tag fluorescence tag visualisation by fluorescence tag fluorescence Lu S., Ye Q., Singh D., Cao Y., Diedrich JK., Yates JR., Villa E., Cleveland DW., Corbett KD. Virus - Publications including interactions involving viral proteins dcleveland@health.ucsd.edu, kcorbett@health.ucsd.edu Nature communications 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus lu-2021-8 in vitro In vitro 3d-em-tomo electron tomography 3D-EM-tomo predetermined predetermined participant predetermined Lu S., Ye Q., Singh D., Cao Y., Diedrich JK., Yates JR., Villa E., Cleveland DW., Corbett KD. Virus - Publications including interactions involving viral proteins dcleveland@health.ucsd.edu, kcorbett@health.ucsd.edu Nature communications 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus 17mer_ssrna 17mer_ssRNA rna ribonucleic acid RNA rna synthetic construct synthetic construct AAGCAGCUAAGAGCGAA ncap_sars2 Nucleoprotein N Nucleocapsid protein protein protein SARS-CoV-2 SARS-CoV-2 SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 2019-nCoV MSDNGPQNQRNAPRITFGGPSDSTGSNQNGERSGARSKQRRPQGLPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAADLDDFSKQLQQSMSSADSTQA nc_045512.2 rna ribonucleic acid RNA rna SARS-CoV-2 SARS-CoV-2 SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 2019-nCoV vme1_sars2 Membrane protein E1 glycoprotein Matrix glycoprotein Membrane glycoprotein M protein protein SARS-CoV-2 SARS-CoV-2 SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 2019-nCoV MADSNGTITVEELKKLLEQWNLVIGFLFLTWICLLQFAYANRNRFLYIIKLIFLWLLWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLFARTRSMWSFNPETNILLNVPLHGTILTRPLLESELVIGAVILRGHLRIAGHHLGRCDIKDLPKEITVATSRTLSYYKLGASQRVAGDSGFAAYSRYRIGNYKLNTDHSSSSDNIALLVQ 17mer_ssrna-n-2 3974090 N/A 3974099 unspecified role unspecified role neutral component neutral component purified purified 3-prime fluorescein fluorescein label fluorescein certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus cy5 label cy5 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 1A phase separation was inhibited at > 5 uM 17-mer RNA. n-n-23 3974090 N/A 3974101 unspecified role unspecified role neutral component neutral component purified purified PS576 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region cy3 label cy3 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false 5-prime UTR sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false 5-prime UTR sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus cy5 label cy5 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 1C-D The addition of viral RNA fragments containing the 5′-UTR to N protein induced the formation of round condensates (Fig. 1c). Addition of the PS576 fragment caused the formation of more amorphous structures resembling a fibrillar network (Fig. 1c). n-n-25 3974090 N/A 3974101 unspecified role unspecified role neutral component neutral component purified purified region cy3 label cy3 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false 5-prime UTR sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus cy5 label cy5 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 1E, Supp. figure 1D, 10A Addition of 1,6-hexanediol (CHEBI:43078);caused droplet dissolution. 17mer_ssrna-n-4 3974090 N/A 3974099 unspecified role unspecified role neutral component neutral component purified purified 3-prime fluorescein fluorescein label fluorescein certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 3A-L Several domains from N protein contribute to RNA-mediated phase separation. Most N protein truncations lacking the L/Q-rich region (residues 210–246) failed to form condensates with RNA. n-n-28 3974090 N/A 3974101 unspecified role unspecified role neutral component neutral component purified purified region cy3 label cy3 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false 5-prime UTR sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified P0DTC9:p.Ser176_Ser206delinsAlaArgGlyGlyAlaGlnAlaAlaAlaArgAlaAlaAlaArgAlaArgAsnAlaAlaArgAsnAlaThrProGlyAlaAlaArgGlyThrAla mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false P0DTC9:p.Ser176_Ser206delinsAspArgGlyGlyAspGlnAlaAspAspArgAspAspAspArgAspArgAsnAspAspArgAsnAspAspThrProGlynullSerSerArgGlyThrSer mutation increasing strength mutation increasing interaction strength mutation increasing strength certain certain sequence position certain certain certain sequence position certain false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 3 M-P, R, Supp. figure 3F Several domains from N protein contribute to RNA-mediated phase separation. The Delta S/R construct showed significant aggregation on its own - in the absence of RNA. n-vme1_sars2-1 3974090 N/A 3974102 unspecified role unspecified role neutral component neutral component purified purified intracytoplasmic/intravirion domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n-terminus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus cy5 label cy5 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 7B, Supp. figure 9 B While purified GFP-M (104–222) did not form condensates on its own or with added RNA, it induced formation of condensates with the N protein even in the absence of RNA. n-vme1_sars2-2 3974090 N/A 3974102 unspecified role unspecified role neutral component neutral component purified purified intracytoplasmic/intravirion domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n-terminus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 7 C-J While purified GFP-M (104–222) did not form condensates on its own or with added RNA, it induced formation of condensates with the N protein even in the absence of RNA. 17mer_ssrna-n-6 3974090 N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus cy5 label cy5 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus cy5 label cy5 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supplementary Fig. 1a Purified N formed condensates without addition of RNA, only at very low salt concentrations (20–40 mM KCl), but these were much smaller and fewer than those formed in the presence of RNA. n-nc_045512.2-2 3974090 N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus alexa 488 label alexa 488 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) N/A 3974101 unspecified role unspecified role neutral component neutral component purified purified region cy3 label cy3 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false 5-prime UTR sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus cy5 label cy5 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supp. figure 2C Soluble N protein was incorporated very slowly into preexisting N + RNA condensates. n-nc_045512.2-3 3974090 N/A 3974101 unspecified role unspecified role neutral component neutral component purified purified region cy3 label cy3 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false 5-prime UTR sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus cy5 label cy5 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) N/A 3974102 unspecified role unspecified role neutral component neutral component purified purified intracytoplasmic/intravirion domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n-terminus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) physical association physical association false false false Supp. figure 10 A/B When GFP-M (104–222) was added to existing condensates of N +RNA-UTR265, it formed a stable annular shell on the condensate surface. When all three molecules were mixed simultaneously, RNA and M formed mutually exclusive condensates with N. 17mer_ssrna-n-1 3974091 N/A 3974099 unspecified role unspecified role neutral component neutral component purified purified 3-prime fluorescein fluorescein label fluorescein certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus cy5 label cy5 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 1 A phase separation was inhibited at > 5 uM 17-mer RNA. n-n-24 3974091 N/A 3974101 unspecified role unspecified role neutral component neutral component purified purified region cy3 label cy3 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false 5-prime UTR sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus cy5 label cy5 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 1E, supp. figure 10A Addition of 1,6-hexanediol (CHEBI:43078);caused droplet dissolution. 17mer_ssrna-n-5 3974091 N/A 3974099 unspecified role unspecified role neutral component neutral component purified purified 3-prime fluorescein fluorescein label fluorescein certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 3A-L Several domains from N protein contribute to RNA-mediated phase separation. n-n-29 3974091 N/A 3974101 unspecified role unspecified role neutral component neutral component purified purified region cy3 label cy3 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false 5-prime UTR sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified P0DTC9:p.Ser176_Ser206delinsAlaArgGlyGlyAlaGlnAlaAlaAlaArgAlaAlaAlaArgAlaArgAsnAlaAlaArgAsnAlaThrProGlyAlaAlaArgGlyThrAla mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false P0DTC9:p.Ser176_Ser206delinsAspArgGlyGlyAspGlnAlaAspAspArgAspAspAspArgAspArgAsnAspAspArgAsnAspAspThrProGlynullSerSerArgGlyThrSer mutation increasing strength mutation increasing interaction strength mutation increasing strength certain certain sequence position certain certain certain sequence position certain false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 3 M-P, Supp. figure 3F Several domains from N protein contribute to RNA-mediated phase separation. Figure 3M:The Delta S/R construct showed significant aggregation on its own - in the absence of RNA. n-vme1_sars2-3 3974091 N/A 3974102 unspecified role unspecified role neutral component neutral component purified purified intracytoplasmic/intravirion domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n-terminus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false intracytoplasmic/intravirion domain required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 7 C-J While purified GFP-M (104–222) did not form condensates on its own or with added RNA, it induced formation of condensates with the N protein even in the absence of RNA. 17mer_ssrna-n-3 3974092 N/A 3974099 unspecified role unspecified role neutral component neutral component purified purified 3-prime fluorescein fluorescein label fluorescein certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus cy5 label cy5 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 2A,B, Supplementary Fig. 2a, b In condensates formed with the short 17-mer RNA, the RNA was highly mobile and freely exchanged;the mobility of this short RNA decreased with longer incubation times, indicating that initial highly dynamic condensates mature over time to a structure with slower dynamics (Supplementary Fig. 2a, b). n-n-26 3974092 N/A 3974101 unspecified role unspecified role neutral component neutral component purified purified PS576 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region cy3 label cy3 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false 5-prime UTR sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false 5-prime UTR sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus cy5 label cy5 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 2C-E n-n-36 3974092 N/A 3974100 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed clover tag gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P0DTC9:p.Ser176_Ser206delinsAlaArgGlyGlyAlaGlnAlaAlaAlaArgAlaAlaAlaArgAlaArgAsnAlaAlaArgAsnAlaThrProGlyAlaAlaArgGlyThrAla mutation increasing strength mutation increasing interaction strength mutation increasing strength certain certain sequence position certain certain certain sequence position certain false P0DTC9:p.Ser176_Ser206delinsAspArgGlyGlyAspGlnAlaAspAspArgAspAspAspArgAspArgAsnAspAspArgAsnAspAspThrProGlynullSerSerArgGlyThrSer mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Delta S/R region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false N/A 3974100 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed clover tag gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P0DTC9:p.Ser176_Ser206delinsAlaArgGlyGlyAlaGlnAlaAlaAlaArgAlaAlaAlaArgAlaArgAsnAlaAlaArgAsnAlaThrProGlyAlaAlaArgGlyThrAla mutation increasing strength mutation increasing interaction strength mutation increasing strength certain certain sequence position certain certain certain sequence position certain false P0DTC9:p.Ser176_Ser206delinsAspArgGlyGlyAspGlnAlaAspAspArgAspAspAspArgAspArgAsnAspAspArgAsnAspAspThrProGlynullSerSerArgGlyThrSer mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Delta S/R region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false direct interaction direct interaction false false false Supp. figure 5 C/D N14SA and N-Delta_SR mutants formed large, dense condensates in nearly 100% of cells, that show slow and incomplete fluorescence recovery in FRAP analysis. n-vme1_sars2-5 3974092 N/A 3974102 unspecified role unspecified role neutral component neutral component purified purified intracytoplasmic/intravirion domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n-terminus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus cy5 label cy5 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supp. figure 9C n-nc_045512.2-5 3974092 N/A 3974101 unspecified role unspecified role neutral component neutral component purified purified region cy3 label cy3 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false 5-prime UTR sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus cy5 label cy5 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) N/A 3974102 unspecified role unspecified role neutral component neutral component purified purified intracytoplasmic/intravirion domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n-terminus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) physical association physical association false false false Supp. figure 10 D/E n-vme1_sars2-4 3974093 N/A 3974102 unspecified role unspecified role neutral component neutral component purified purified intracytoplasmic/intravirion domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n-terminus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus cy5 label cy5 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) N/A 3974101 unspecified role unspecified role neutral component neutral component purified purified region cy3 label cy3 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false 5-prime UTR sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false in vitro In vitro physical association physical association false false false 7L n-n-34 3974093 N/A 3974101 unspecified role unspecified role neutral component neutral component purified purified region cy3 label cy3 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false 5-prime UTR sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus cy5 label cy5 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supp. figure 1E n-nc_045512.2-4 3974093 N/A 3974101 unspecified role unspecified role neutral component neutral component purified purified region cy3 label cy3 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false PS576 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus cy5 label cy5 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) N/A 3974102 unspecified role unspecified role neutral component neutral component purified purified intracytoplasmic/intravirion domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n-terminus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) physical association physical association false false false Supp. figure 10 C When all three molecules were mixed simultaneously, RNA and M formed mutually exclusive condensates with N. n-n-30 3974094 N/A 3974101 unspecified role unspecified role neutral component neutral component purified purified PS576 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false 5-prime UTR sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified Lys256 cross linker cross linker crosslinker crosslinker certain certain sequence position certain certain certain sequence position certain false Lys248 cross linker cross linker crosslinker crosslinker certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified Lys256 cross linker cross linker crosslinker crosslinker certain certain sequence position certain certain certain sequence position certain false Lys249 cross linker cross linker crosslinker crosslinker certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) 3974269 3974266 3974270 3974267 direct interaction direct interaction false false false 4, Supplementary Table 2, Supplementary Fig. 4, Supplementary Data 1 Two cross-links (K256–K256 and K248–K249) were significantly enriched upon RNA-mediated condensation in multiple samples. n-n-31 3974094 N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified Lys256 cross linker cross linker crosslinker crosslinker certain certain sequence position certain certain certain sequence position certain false Lys248 cross linker cross linker crosslinker crosslinker certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified Lys256 cross linker cross linker crosslinker crosslinker certain certain sequence position certain certain certain sequence position certain false Lys249 cross linker cross linker crosslinker crosslinker certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) 3974276 3974273 3974277 3974274 direct interaction direct interaction false false false 4, Supplementary Table 2, Supplementary Fig. 4, Supplementary Data 1 Two cross-links (K256–K256 and K248–K249) were significantly enriched upon RNA-mediated condensation in multiple samples. n-n-27 3974095 N/A 3974101 unspecified role unspecified role neutral component neutral component purified purified 5-prime UTR sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supplementary figure 1B/C Addition of RNA enhanced condensate formation at salt concentrations approaching physiological (>80 mM KCl). n-n-33 3974095 N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified Delta S/R region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified Delta S/R region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supplementary figure 1B, 3E The Delta S/R construct showed significant aggregation on its own - in the absence of RNA. n-n-35 3974096 N/A 3974100 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed clover tag gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P0DTC9:p.Ser176_Ser206delinsAlaArgGlyGlyAlaGlnAlaAlaAlaArgAlaAlaAlaArgAlaArgAsnAlaAlaArgAsnAlaThrProGlyAlaAlaArgGlyThrAla mutation increasing strength mutation increasing interaction strength mutation increasing strength certain certain sequence position certain certain certain sequence position certain false P0DTC9:p.Ser176_Ser206delinsAspArgGlyGlyAspGlnAlaAspAspArgAspAspAspArgAspArgAsnAspAspArgAsnAspAspThrProGlynullSerSerArgGlyThrSer mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Delta S/R region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false N/A 3974100 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed clover tag gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P0DTC9:p.Ser176_Ser206delinsAlaArgGlyGlyAlaGlnAlaAlaAlaArgAlaAlaAlaArgAlaArgAsnAlaAlaArgAsnAlaThrProGlyAlaAlaArgGlyThrAla mutation increasing strength mutation increasing interaction strength mutation increasing strength certain certain sequence position certain certain certain sequence position certain false P0DTC9:p.Ser176_Ser206delinsAspArgGlyGlyAspGlnAlaAspAspArgAspAspAspArgAspArgAsnAspAspArgAsnAspAspThrProGlynullSerSerArgGlyThrSer mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Delta S/R region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false colocalization colocalization false false false 5 A/B The phosphorylation-resistant N14SA mutant, and a deletion mutant of the S/R-rich region (residues 176–206) formed large, dense condensates in nearly 100% of cells. n-n-37 3974096 N/A 3974100 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed clover tag gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false N/A 3974100 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed clover tag gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false colocalization colocalization false false false Supp. figure 6 C/D Kenpaullone (CHEBI:131490) Kenpaullone (CHEBI:131490) in combination with SRPIN340 a selective serine-arginine protein kinase 1/2 (SRPK1/2) inhibitor. (CHEMBL4064277) n-n-32 3974097 N/A 3974100 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed clover tag gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P0DTC9:p.Ser176_Ser206delinsAlaArgGlyGlyAlaGlnAlaAlaAlaArgAlaAlaAlaArgAlaArgAsnAlaAlaArgAsnAlaThrProGlyAlaAlaArgGlyThrAla mutation increasing strength mutation increasing interaction strength mutation increasing strength certain certain sequence position certain certain certain sequence position certain false P0DTC9:p.Ser176_Ser206delinsAspArgGlyGlyAspGlnAlaAspAspArgAspAspAspArgAspArgAsnAspAspArgAsnAspAspThrProGlynullSerSerArgGlyThrSer mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Delta S/R region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false N/A 3974100 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed clover tag gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false P0DTC9:p.Ser176_Ser206delinsAlaArgGlyGlyAlaGlnAlaAlaAlaArgAlaAlaAlaArgAlaArgAsnAlaAlaArgAsnAlaThrProGlyAlaAlaArgGlyThrAla mutation increasing strength mutation increasing interaction strength mutation increasing strength certain certain sequence position certain certain certain sequence position certain false P0DTC9:p.Ser176_Ser206delinsAspArgGlyGlyAspGlnAlaAspAspArgAspAspAspArgAspArgAsnAspAspArgAsnAspAspThrProGlynullSerSerArgGlyThrSer mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Delta S/R region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false 5 C/D N14SA and N-Delta_SR mutants formed large, dense condensates in nearly 100% of cells, that show slow and incomplete fluorescence recovery in FRAP analysis. n-nc_045512.2-1 3974098 N/A 3974101 unspecified role unspecified role neutral component neutral component purified purified region cy3 label cy3 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false PS576 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false in vitro In vitro N/A 3974100 unspecified role unspecified role neutral component neutral component purified purified n-terminus cy5 label cy5 label n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 1F, Supplementary Fig. 1f–g Cryo-ET of N protein + RNA condensates revealed well-defined texture suggestive of internal order, which was also observed by super-resolution light microscopy (Fig. 1f and Supplementary Fig. 1e–g).