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/ Multiple Roles of SARS-CoV-2 N Protein Facilitated by Proteoform-Specific Interactions with RNA, Host Proteins, and Convalescent Antibodies. Multiple Roles of SARS-CoV-2 N Protein Facilitated by Proteoform-Specific Interactions with RNA, Host Proteins, and Convalescent Antibodies. JACS Au 2021 imex curation Lutomski CA., El-Baba TJ., Bolla JR., Robinson CV. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus carol.robinson@chem.ox.ac.uk Only protein-protein interactions imex curation ecoli Escherichia coli (strain K12) ms of complexes mass spectrometry studies of complexes ms of complexes predetermined predetermined participant predetermined pH 5.0, 7.4, and 8.0 8.0 7.4 7.4 and 8.0 5.0 Lutomski CA., El-Baba TJ., Bolla JR., Robinson CV. Virus - Publications including interactions involving viral proteins carol.robinson@chem.ox.ac.uk Accepted 2021-OCT-11 AT 11:03 BST AT 11:03 BST by ORCHARD JACS Au 2021 Only protein-protein interactions imex curation imex curation Multiple Roles of SARS-CoV-2 N Protein Facilitated by Proteoform-Specific Interactions with RNA, Host Proteins, and Convalescent Antibodies. Multiple Roles of SARS-CoV-2 N Protein Facilitated by Proteoform-Specific Interactions with RNA, Host Proteins, and Convalescent Antibodies. JACS Au 2021 imex curation Lutomski CA., El-Baba TJ., Bolla JR., Robinson CV. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus carol.robinson@chem.ox.ac.uk Only protein-protein interactions imex curation 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 Accepted 2021-OCT-11 AT 11:03 BST AT 11:03 BST by ORCHARD JACS Au 2021 Only protein-protein interactions imex curation imex curation 4 × gagaa rna ribonucleic acid RNA rna chemical synthesis Chemical synthesis (Chemical synthesis) GAGAAGAGAAGAGAAGAGAA 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 cyclosporin_a Cyclosporin A small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) 4 × gaugg rna ribonucleic acid RNA rna chemical synthesis Chemical synthesis (Chemical synthesis) GAUGGGAUGGGAUGGGAUGG 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 DIP protein P62937 original sequence version: 81 DIP protein P62937-1 original sequence version: 141 9B2E637A555E4434 n-105 1 9 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 direct interaction direct interaction 4 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-106 7 9 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 direct interaction direct interaction Supp. figure 4/5. Table S6 Low abundance of the dimer. n-107 1 9 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 direct interaction direct interaction 6 Supp. figure 7, Table S6 n-108 1 9 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 direct interaction direct interaction 4 Supp. figure 7, Table S6 n-109 1 9 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 direct interaction direct interaction 3 Supp. figure 7, Table S6 n-110 1 9 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 direct interaction direct interaction 3 Supp. figure 7, Table S6 4 gaugg-n-1 7 11 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 9 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 region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) direct interaction direct interaction Figure 2, Supp. figure 9, 10, Table S7 4 gaugg-n-2 7 11 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 9 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 region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) direct interaction direct interaction Figure 2, Supp. figure 9, 10, Table S7 N1–209 bound to two 4 × −GAUGG RNA is the predominant species. 4 gagaa-n-1 7 8 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 9 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 region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) direct interaction direct interaction Figure 2, Supp. figure 9, 10, Table S7 4 gaugg-n-3 7 11 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 9 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction Figure 2C 4 gagaa-n-2 7 8 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 9 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction Supp. figure 11, Table S7 n-ppia-5 7 12 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 ecoli Escherichia coli (strain K12) 9 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction Figure 3A CypA did not interact with N1–220, N1–273, nor full-length N under the same conditions. n-ppia-6 7 9 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 ecoli Escherichia coli (strain K12) 9 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction Figure 3A n-ppia-7 7 12 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 ecoli Escherichia coli (strain K12) 12 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction Figure 3A, Supp. figure 12,13. n-ppia-8 7 10 competitor competitor competitor neutral component neutral component purified purified tolin Tolypocladium inflatum 9 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 ecoli Escherichia coli (strain K12) 12 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction Figure 3B cyclosporin_a-n-1 7 10 unspecified role unspecified role neutral component neutral component purified purified tolin Tolypocladium inflatum 12 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction Figure 3B, table 2 CypA (Cyclophilin A) preferentially binds CsA (Cyclosporin A). n-111 7 9 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 ecoli Escherichia coli (strain K12) direct interaction direct interaction Supp. figure 14 n-112 1 9 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 direct interaction direct interaction 3 Supp. figure 7, Table S6