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/ lutomski-2021-2 in vitro In vitro ms of complexes mass spectrometry studies of complexes ms of complexes predetermined predetermined participant predetermined Lutomski CA., El-Baba TJ., Bolla JR., Robinson CV. Virus - Publications including interactions involving viral proteins carol.robinson@chem.ox.ac.uk JACS Au 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus lutomski-2021-1 ecoli Escherichia coli (strain K12) ms of complexes mass spectrometry studies of complexes ms of complexes predetermined predetermined participant predetermined Lutomski CA., El-Baba TJ., Bolla JR., Robinson CV. Virus - Publications including interactions involving viral proteins carol.robinson@chem.ox.ac.uk JACS Au 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus 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 4 × gaugg rna ribonucleic acid RNA rna chemical synthesis Chemical synthesis (Chemical synthesis) GAUGGGAUGGGAUGGGAUGG 4 × gagaa rna ribonucleic acid RNA rna chemical synthesis Chemical synthesis (Chemical synthesis) GAGAAGAGAAGAGAAGAGAA ppia_human Peptidyl-prolyl cis-trans isomerase A Cyclophilin A Cyclosporin A-binding protein PPIA CYPA Rotamase A protein protein human Homo sapiens Human MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE cyclosporin_a Cyclosporin A small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) n-106 4084371 N/A 4084373 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 Stoichiometry: 2.0 direct interaction direct interaction false false false Supp. figure 4/5. Table S6 Low abundance of the dimer. 4 gaugg-n-1 4084371 N/A 4084374 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 N/A 4084373 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 region sufficient to bind sufficient binding region sufficient to bind 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) Stoichiometry: 1.0 direct interaction direct interaction false false false Figure 2, Supp. figure 9, 10, Table S7 4 gaugg-n-2 4084371 N/A 4084374 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 2.0 N/A 4084373 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 region sufficient to bind sufficient binding region sufficient to bind 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) Stoichiometry: 1.0 direct interaction direct interaction false false false Figure 2, Supp. figure 9, 10, Table S7 N1–209 bound to two 4 × −GAUGG RNA is the predominant species. 4 gagaa-n-1 4084371 N/A 4084375 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 N/A 4084373 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 region sufficient to bind sufficient binding region sufficient to bind 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) Stoichiometry: 1.0 direct interaction direct interaction false false false Figure 2, Supp. figure 9, 10, Table S7 4 gaugg-n-3 4084371 N/A 4084374 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 N/A 4084373 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 direct interaction direct interaction false false false Figure 2C 4 gagaa-n-2 4084371 N/A 4084375 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 N/A 4084373 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 direct interaction direct interaction false false false Supp. figure 11, Table S7 n-ppia-5 4084371 N/A 4084376 unspecified role unspecified role neutral component neutral component purified purified n-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-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) Stoichiometry: 1.0 N/A 4084373 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) Stoichiometry: 1.0 direct interaction direct interaction false false false Figure 3A CypA did not interact with N1–220, N1–273, nor full-length N under the same conditions. n-ppia-6 4084371 N/A 4084373 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) Stoichiometry: 1.0 N/A 4084373 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) Stoichiometry: 1.0 direct interaction direct interaction false false false Figure 3A n-ppia-7 4084371 N/A 4084376 unspecified role unspecified role neutral component neutral component purified purified n-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-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) Stoichiometry: 1.0 N/A 4084376 unspecified role unspecified role neutral component neutral component purified purified n-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-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) Stoichiometry: 1.0 direct interaction direct interaction false false false Figure 3A, Supp. figure 12,13. n-ppia-8 4084371 N/A 4084377 competitor competitor competitor neutral component neutral component purified purified tolin Tolypocladium inflatum N/A 4084373 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) N/A 4084376 unspecified role unspecified role neutral component neutral component purified purified n-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-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) direct interaction direct interaction false false false Figure 3B cyclosporin_a-n-1 4084371 N/A 4084377 unspecified role unspecified role neutral component neutral component purified purified tolin Tolypocladium inflatum Stoichiometry: 1.0 N/A 4084376 unspecified role unspecified role neutral component neutral component purified purified n-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-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) Stoichiometry: 1.0 direct interaction direct interaction false false false Figure 3B, table 2 CypA (Cyclophilin A) preferentially binds CsA (Cyclosporin A). n-111 4084371 N/A 4084373 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) Stoichiometry: 2.0 direct interaction direct interaction false false false Supp. figure 14 n-105 4084372 N/A 4084373 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 Stoichiometry: 2.0 direct interaction direct interaction false false false 1, 2C, Table 1, Supp. figure 8 Figure 1;pH value is not stated. Figure S8;pH = 7.4 Mass spectra for full-length N at pH 5.0 and 8.0 reveal broadened and featureless peaks suggesting that NFL is likely aggregated. n-107 4084372 N/A 4084373 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 Stoichiometry: 3.0 direct interaction direct interaction false false false Supp. figure 7, Table S6 n-108 4084372 N/A 4084373 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 Stoichiometry: 3.0 direct interaction direct interaction false false false Supp. figure 7, Table S6 n-109 4084372 N/A 4084373 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 Stoichiometry: 2.0 direct interaction direct interaction false false false Supp. figure 7, Table S6 n-110 4084372 N/A 4084373 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 Stoichiometry: 6.0 direct interaction direct interaction false false false Supp. figure 7, Table S6 n-112 4084372 N/A 4084373 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 Stoichiometry: 3.0 direct interaction direct interaction false false false Supp. figure 7, Table S6