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/ biswal-2021-3 in vitro In vitro crosslink cross-linking study crosslink weight by staining molecular weight estimation by staining weight by staining Biswal M., Diggs S., Xu D., Khudaverdyan N., Lu J., Fang J., Blaha G., Hai R., Song J. Virus - Publications including interactions involving viral proteins Cross linker EGS:ethylene glycol bis(succinimidyl succinate) jikui.song@ucr.edu,ronghai@ucr.edu Nucleic acids research 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus biswal-2021-2 ecoli Escherichia coli (strain K12) molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Biswal M., Diggs S., Xu D., Khudaverdyan N., Lu J., Fang J., Blaha G., Hai R., Song J. Virus - Publications including interactions involving viral proteins jikui.song@ucr.edu,ronghai@ucr.edu Nucleic acids research 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus biswal-2021-4 in vitro In vitro rna rna pol assay rna directed rna polymerase assay rna rna pol assay tag fluorescence tag visualisation by fluorescence tag fluorescence Biswal M., Diggs S., Xu D., Khudaverdyan N., Lu J., Fang J., Blaha G., Hai R., Song J. Virus - Publications including interactions involving viral proteins jikui.song@ucr.edu,ronghai@ucr.edu Nucleic acids research 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus biswal-2021-1 ecoli Escherichia coli (strain K12) x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Biswal M., Diggs S., Xu D., Khudaverdyan N., Lu J., Fang J., Blaha G., Hai R., Song J. Virus - Publications including interactions involving viral proteins jikui.song@ucr.edu,ronghai@ucr.edu Nucleic acids research 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus p0dtd1-pro_0000449626 Non-structural protein 8 rep ORF1ab polyprotein 1a-1b protein protein SARS-CoV-2 SARS-CoV-2 SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 2019-nCoV AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ 3943 4140 p0dtd1-pro_0000449625 Non-structural protein 7 rep ORF1ab polyprotein 1a-1b protein protein SARS-CoV-2 SARS-CoV-2 SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 2019-nCoV SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQ 3860 3942 p0dtd1-pro_0000449629 RNA-directed RNA polymerase nsp12 rep ORF1ab polyprotein 1a-1b protein protein SARS-CoV-2 SARS-CoV-2 SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 2019-nCoV SADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQ 4393 5324 rna_substrate ds rna ds rna double stranded ribonucleic acid chemical synthesis Chemical synthesis (Chemical synthesis) UUUUCAUGCUACGCGUAGUUUUCUACGCG rep-rep-198 4057552 N/A 4057556 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 N/A 4057557 unspecified role unspecified role neutral component neutral component purified purified p.Phe49Ala mutation with complex effect mutation with complex effect certain certain sequence position certain certain certain sequence position certain false p.Leu56Ala mutation with complex effect mutation with complex effect certain certain sequence position certain certain certain sequence position certain false p.Met52Ala mutation with complex effect mutation with complex effect certain certain sequence position certain certain certain sequence position certain false p.Leu71Ala mutation with complex effect mutation with complex effect certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449625:p.Asn37Val 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 p.Cys8Gly mutation with complex effect mutation with complex effect certain certain sequence position certain certain certain sequence position certain false p.Val11Ala mutation with complex effect mutation with complex effect 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 1C, 3 C/E, supp. figure 1C/7A NSP7+8 tetramer Mutations of NSP7 F49A and NSP7 L56A (in Figure 3C) and of NSP8 F92A (in Figure 3D) lead to an increased NSP8 dimerization, accompanied by reduction of the hetero-tetramerization of NSP7–NSP8. Mutations of NSP7, C8G and V11A, lead to an even more pronounced increase of NSP8 homodimer at the expense of NSP7-NSP8 heterotetramer. The NSP7 M52A mutation does not appreciably affect the population of NSP8 dimer, but leads to a substantial heterotetramer-to-heterodimer shift of NSP7-NSP8. The NSP7 L71A mutant increases tetramerization of NSP7 with NSP8. Figure S1C appears to show a decrease in NSP8 dimerization and a slight increase in NSP7+8 dimerization. rep-rep-199 4057552 N/A 4057556 unspecified role unspecified role neutral component neutral component purified purified P0DTD1-PRO_0000449626:p.Met90Ala 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 P0DTD1-PRO_0000449626:p.Phe92Ala 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 P0DTD1-PRO_0000449626:p.Met94Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 N/A 4057557 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 direct interaction direct interaction false false false 1C, 3F NSP7+8 dimer rep-rep-200 4057552 N/A 4057556 unspecified role unspecified role neutral component neutral component purified purified P0DTD1-PRO_0000449626:p.Phe92Ala mutation increasing strength mutation increasing interaction strength mutation increasing strength certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449626:p.Met90Ala mutation increasing strength mutation increasing interaction strength mutation increasing strength certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449626:p.Met94Ala mutation increasing strength mutation increasing interaction strength mutation increasing strength 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 1C, 3 D/F NSP8 dimer rep-201 4057552 N/A 4057556 unspecified role unspecified role neutral component neutral component purified purified P0DTD1-PRO_0000449626:p.Met90Ala mutation increasing strength mutation increasing interaction strength mutation increasing strength certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449626:p.Met94Ala mutation increasing strength mutation increasing interaction strength mutation increasing strength certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 4.0 direct interaction direct interaction false false false 1C, 3F NSP8 tetramer rep-rep-201 4057552 N/A 4057556 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 N/A 4057557 unspecified role unspecified role neutral component neutral component purified purified P0DTD1-PRO_0000449625:p.Met52Ala mutation increasing strength mutation increasing interaction strength mutation increasing strength certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449625:p.Asn37Val 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 P0DTD1-PRO_0000449625:p.Phe49Ala 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 P0DTD1-PRO_0000449625:p.Leu56Ala 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 P0DTD1-PRO_0000449625:p.Cys8Gly mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449625:p.Val11Ala mutation increasing strength mutation increasing interaction strength mutation increasing strength 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 1C, 3 C/E, Supp. figure 7A NSP7+8 dimer rep-rep-202 4057552 N/A 4057556 unspecified role unspecified role neutral component neutral component purified purified p.Phe92Ala mutation with complex effect mutation with complex effect certain certain sequence position certain certain certain sequence position certain false p.Met90Ala mutation with complex effect mutation with complex effect certain certain sequence position certain certain certain sequence position certain false p.Met94Ala mutation with complex effect mutation with complex effect certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 N/A 4057557 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 1C, 3 D/F NSP7+8 tetramer Mutations of NSP7 F49A and NSP7 L56A (in Figure 3C) and of NSP8 F92A (in Figure 3D) lead to an increased NSP8 dimerization, accompanied by reduction of the hetero-tetramerization of NSP7–NSP8. Mutations M90A and M94A, lead to an increased NSP8 dimer formation at the expense of the NSP7–NSP8 heterotetramer. rep-rep-207 4057552 N/A 4057556 unspecified role unspecified role neutral component neutral component purified purified C-terminal region/delta73 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 N/A 4057557 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 4F NSP7+8 tetramer rep-rep-208 4057552 N/A 4057556 unspecified role unspecified role neutral component neutral component purified purified C-terminal region/delta73 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 4057557 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 direct interaction direct interaction false false false supp. figure 4F NSP7+8 dimer rep-209 4057552 N/A 4057556 unspecified role unspecified role neutral component neutral component purified purified C-terminal region/delta73 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 4f NSP8 dimer rep-rep-197 4057553 N/A 4057556 unspecified role unspecified role neutral component neutral component purified purified C-terminal region/delta73 sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false Stoichiometry: 2.0 N/A 4057557 unspecified role unspecified role neutral component neutral component purified purified Stoichiometry: 2.0 direct interaction direct interaction false false false 1B, Supp. figure 4E The NSP7-NSP8 mixture eluted at a volume corresponding to what is expected for a 2:2 tetrameric form (∼62 kDa). rep-rep-205 4057553 N/A 4057556 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 N/A 4057557 unspecified role unspecified role neutral component neutral component purified purified P0DTD1-PRO_0000449625:p.Phe49Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449625:p.Leu56Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449625:p.Met52Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449625:p.Cys8Gly mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449625:p.Val11Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449625:p.Asn37Val 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 ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 direct interaction direct interaction false false false supp. figure 3/7B NSP7+8 tetramer;mutations on the interface II of NSP7 lead to even more severe loss of the tetrameric NSP7–NSP8 fraction than mutations on interface I. rep-rep-206 4057553 N/A 4057556 unspecified role unspecified role neutral component neutral component purified purified P0DTD1-PRO_0000449626:p.Met90Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449626:p.Phe92Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449626:p.Met94Ala mutation decreasing strength mutation decreasing interaction strength mutation decreasing strength certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 N/A 4057557 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 3 NSP7+8 tetramer. rep-rep-209 4057553 N/A 4057556 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 n-terminus sumo tag sumo tag SUMO tag sumo tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false N/A 4057558 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 n-terminus sumo tag sumo tag SUMO tag sumo tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false N/A 4057557 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 n-terminus sumo tag sumo tag SUMO tag sumo tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false physical association physical association false false false Supp. figure 7 C/D It is stated that the NSP7N37V mutation leads to a modest, but notable, disruption of the NSP7-NSP8-NSP12 complex. rep-rep-203 4057554 N/A 4057559 enzyme target enzyme target substrate substrate neutral component neutral component 5' FAM fluorescein fluorescein label fluorescein certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) N/A 4057557 stimulator stimulator ancillary ancillary purified purified P0DTD1-PRO_0000449625:p.[Phe49Ala;Met52Ala;Leu56Ala] mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449625:p.Cys8Gly mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449625:p.Phe49Ala mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449625:p.Met52Ala mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449625:p.Leu56Ala mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449625:p.Val11Ala mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449625:p.Asn37Val mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 4057556 stimulator stimulator ancillary ancillary purified purified ecoli Escherichia coli (strain K12) N/A 4057558 enzyme enzyme neutral component neutral component purified purified ecoli Escherichia coli (strain K12) rna elongation rna strand elongation rna elongation false false false 5, (Supp. figure 8B) Similar results were obtained using WT bacterially optimised NSP12 and "native" NSP12 with sequence from RefSeq identifier NC_045512. rep-rep-204 4057554 N/A 4057559 enzyme target enzyme target substrate substrate neutral component neutral component 5' FAM fluorescein fluorescein label fluorescein certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) N/A 4057557 stimulator stimulator ancillary ancillary purified purified ecoli Escherichia coli (strain K12) N/A 4057556 stimulator stimulator ancillary ancillary purified purified P0DTD1-PRO_0000449626:p.Phe92Ala mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449626:p.Met90Ala mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449626:p.Met94Ala mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449626:p.Lys58Ala mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449626:p.Arg75Ala mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain false P0DTD1-PRO_0000449626:p.Lys82Ala mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 4057558 enzyme enzyme neutral component neutral component purified purified ecoli Escherichia coli (strain K12) rna elongation rna strand elongation rna elongation false false false 5 Similar results were obtained using WT bacterially optimised NSP12 and "native" NSP12 with sequence from RefSeq identifier NC_045512. rep-rep-196 4057555 N/A 4057556 unspecified role unspecified role neutral component neutral component purified purified Stoichiometry: 2.0 N/A 4057557 unspecified role unspecified role neutral component neutral component purified purified Stoichiometry: 2.0 direct interaction direct interaction false false false Table S1