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/ wilamowski-2021-3 in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Wilamowski M., Hammel M., Leite W., Zhang Q., Kim Y., Weiss K., Jedrzejczak R., Rosenberg DJ., Fan Y., Wower J., Bierma J., Sarker AH., Tsutakawa SE., Pingali SV., O'Neill HM., Joachimiak A., Hura GL. Coronavirus - Interactions investigated in the context of Coronavirus SEC-MALS (Size Exclusion Chromatography with MultiAngle Light Scattering). oneillhm@ornl.gov, andrzejj@anl.gov, glhura@lbl.gov Biophysical journal 2021 Only protein-protein interactions imex curation imex curation Virus - Publications including interactions involving viral proteins wilamowski-2021-4 in vitro In vitro saxs x ray scattering saxs predetermined predetermined participant predetermined Wilamowski M., Hammel M., Leite W., Zhang Q., Kim Y., Weiss K., Jedrzejczak R., Rosenberg DJ., Fan Y., Wower J., Bierma J., Sarker AH., Tsutakawa SE., Pingali SV., O'Neill HM., Joachimiak A., Hura GL. Coronavirus - Interactions investigated in the context of Coronavirus oneillhm@ornl.gov, andrzejj@anl.gov, glhura@lbl.gov Biophysical journal 2021 Only protein-protein interactions imex curation imex curation Virus - Publications including interactions involving viral proteins wilamowski-2021-5 in vitro In vitro sans small angle neutron scattering SANS SANS sans predetermined predetermined participant predetermined Wilamowski M., Hammel M., Leite W., Zhang Q., Kim Y., Weiss K., Jedrzejczak R., Rosenberg DJ., Fan Y., Wower J., Bierma J., Sarker AH., Tsutakawa SE., Pingali SV., O'Neill HM., Joachimiak A., Hura GL. Coronavirus - Interactions investigated in the context of Coronavirus oneillhm@ornl.gov, andrzejj@anl.gov, glhura@lbl.gov Biophysical journal 2021 Only protein-protein interactions imex curation imex curation Virus - Publications including interactions involving viral proteins wilamowski-2021-6 in vitro In vitro emsa electrophoretic mobility shift assay Gel retardation assay band shift band shift Gel retardation assay emsa tag visualisation tag visualisation Wilamowski M., Hammel M., Leite W., Zhang Q., Kim Y., Weiss K., Jedrzejczak R., Rosenberg DJ., Fan Y., Wower J., Bierma J., Sarker AH., Tsutakawa SE., Pingali SV., O'Neill HM., Joachimiak A., Hura GL. Coronavirus - Interactions investigated in the context of Coronavirus oneillhm@ornl.gov, andrzejj@anl.gov, glhura@lbl.gov Biophysical journal 2021 Only protein-protein interactions imex curation imex curation Virus - Publications including interactions involving viral proteins wilamowski-2021-2 ecoli Escherichia coli (strain K12) x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Wilamowski M., Hammel M., Leite W., Zhang Q., Kim Y., Weiss K., Jedrzejczak R., Rosenberg DJ., Fan Y., Wower J., Bierma J., Sarker AH., Tsutakawa SE., Pingali SV., O'Neill HM., Joachimiak A., Hura GL. Coronavirus - Interactions investigated in the context of Coronavirus oneillhm@ornl.gov, andrzejj@anl.gov, glhura@lbl.gov Biophysical journal 2021 Only protein-protein interactions imex curation imex curation Virus - Publications including interactions involving viral proteins wilamowski-2021-7 in vitro In vitro rna rna pol assay rna directed rna polymerase assay rna rna pol assay weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra Wilamowski M., Hammel M., Leite W., Zhang Q., Kim Y., Weiss K., Jedrzejczak R., Rosenberg DJ., Fan Y., Wower J., Bierma J., Sarker AH., Tsutakawa SE., Pingali SV., O'Neill HM., Joachimiak A., Hura GL. Coronavirus - Interactions investigated in the context of Coronavirus oneillhm@ornl.gov, andrzejj@anl.gov, glhura@lbl.gov Biophysical journal 2021 Only protein-protein interactions imex curation imex curation Virus - Publications including interactions involving viral proteins 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_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 long_ssrna oligo rna ribonucleic acid RNA rna chemical synthesis Chemical synthesis (Chemical synthesis) UUUUCAUGCUACGCGUAGCAUGCUACGCGUAGCAUG short_ssrna oligo rna ribonucleic acid RNA rna chemical synthesis Chemical synthesis (Chemical synthesis) CAUGCUACGCGUAGCAUGCUACGCGUAG 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 31mer_hairpin_rna rna ribonucleic acid RNA rna in vitro In vitro GGCUUAGGAGAUGAUGAAAGUCAUUCUCCU residues 9-23 map to MW365029.1 (SARS-CoV-2/human/CHL/Santiago-PUC_MVL_0400/2020) rep-rep-212 4067965 N/A 4067971 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 3A,2, 4A bottom, 5A bottom, supp. figure 2, table S2 Nsp7 forms multimers and dimers. rep-213 4067965 N/A 4067971 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) N/A 4067971 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 3A,2, Supp. figure 2, table S2 Nsp7 forms multimers and dimers. rep-rep-213 4067965 N/A 4067972 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 3A,2, table S2 Nsp8 forms concentration-dependent oligomers in solution. rep-216 4067965 N/A 4067972 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) N/A 4067972 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 3A,2, 4A, table S2 Nsp8 forms concentration-dependent oligomers in solution. Figure 3A: In this figure Nsp8 appears to form one peak with an M.Wt of ~110 kDa. (calculated M. Wt of monomer is ~22kDa) Figure 4A also shows one peak for Nsp8, but as there are no values given for M.Wt values on the upper part of the X-axis, is it not possible to estimate the M.wt of this peak. rep-rep-215 4067965 N/A 4067972 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) N/A 4067971 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 4A, bottom,Table S2 A transient complex composed of oligomers and free proteins. long_ssrna oligo-rep-1 4067965 N/A 4067973 unspecified role unspecified role neutral component neutral component whole molecule sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 N/A 4067972 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 4A top, 2, Supp. figure 5,Table S2 Neither Figure 2 or 4 (Supp. figure 5) indicate which form of ssRNA was used, but the text states:- "Nsp8 did bind the long ssRNA, but not the short ssRNA, at high affinity. The mixture of Nsp8 with long ssRNA shows only one distinct peak, consistent with the 1:1 complex." long_ssrna oligo-rep-2 4067965 N/A 4067971 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) N/A 4067974 unspecified role unspecified role neutral component neutral component whole molecule sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) N/A 4067973 unspecified role unspecified role neutral component neutral component whole molecule sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) N/A 4067972 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) 4067999 4067997 direct interaction direct interaction false false false 4A bottom, 2 These experiments do not support a stable ternary Nsp7/8 dsRNA complex. rep-rep-217 4067965 N/A 4067975 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 N/A 4067972 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 5A top, table S2 There is no Nsp8/12 interaction with RNA. long_ssrna oligo-rep-3 4067965 N/A 4067975 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 N/A 4067971 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 N/A 4067974 unspecified role unspecified role neutral component neutral component whole molecule sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 N/A 4067973 unspecified role unspecified role neutral component neutral component whole molecule sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 N/A 4067972 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 4068010 4068008 direct interaction direct interaction false false false 5A bottom, 2, Table S2 The addition of dsRNA or ssRNA stabilizes the Nsp7/8/12/RNA within a 1:2:1:1 complex;unfortunately the identity of the ssRNA is not stated. long_ssrna oligo-rep-6 4067965 N/A 4067974 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) N/A 4067973 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction false false false Supp. figure 3 long_ssrna oligo-rep-7 4067965 N/A 4067975 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) N/A 4067971 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) N/A 4067972 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 5A bottom, 2, Supp. figure 7, Table S2 A heterogeneous and weak Nsp7/8/12 complex. Nsp7/8/12 does not form a stable structure until RNA is present. The first SEC trace, shows a split peak and tail with a significant peak from Nsp7 at later elution times, already suggesting transient dissociation of Nsp7 from the Nsp8/12 complex. rep-rep-211 4067966 N/A 4067972 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) N/A 4067971 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 4B,2, table S2 rep-214 4067966 N/A 4067971 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 3B,2, Supp. figure 2B, table S2 Best-fit model for Nsp7 is an alternate dimer. rep-215 4067966 N/A 4067972 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 3B,2, Supp. figure 4, table S2 A mixture of the dimer and monomer models fitted the SAXS data for Nsp8 at a 2.5 mg/mL concentration and the SAXS data from the leading edge of the SEC major elution peak. long_ssrna oligo-short_ssrna-1 4067966 N/A 4067974 unspecified role unspecified role neutral component neutral component whole molecule sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 N/A 4067973 unspecified role unspecified role neutral component neutral component whole molecule sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 N/A 4067972 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 4068030 4068028 direct interaction direct interaction false false false 4 B/C, 2, Table S2 long_ssrna oligo-rep-5 4067966 N/A 4067975 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 N/A 4067971 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 N/A 4067974 unspecified role unspecified role neutral component neutral component whole molecule sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 N/A 4067973 unspecified role unspecified role neutral component neutral component whole molecule sufficient to bind sufficient binding region sufficient to bind undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) Stoichiometry: 1.0 N/A 4067972 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 2.0 4068038 4068036 direct interaction direct interaction false false false 5B, 2, Table S2 The addition of dsRNA or ssRNA stabilizes the Nsp7/8/12/RNA within a 1:2:1:1 complex;unfortunately the identity of the ssRNA is not stated. rep-rep-218 4067966 N/A 4067975 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) Stoichiometry: 1.0 N/A 4067972 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 5B, table S2 long_ssrna oligo-short_ssrna oligo-1 4067966 N/A 4067973 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) N/A 4067974 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction false false false Supp. figure 3, figure 2. rep-rep-214 4067967 N/A 4067972 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) N/A 4067971 unspecified role unspecified role neutral component neutral component purified purified region 2h label 2h label deuterium D2 2H2 2H2 deuterium D2 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 2, 3F, 4G, Table S2 Nsp7 dramatically modifies Nsp8 conformation or assembly. rep-rep-216 4067967 N/A 4067972 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 2, Table S2 M. Wt for Nsp8 is given as 38 kDa for SANS in table S2. (Monomer =24kDa) rep-short_ssrna oligo-1 4067968 N/A 4067974 unspecified role unspecified role bait bait region radiolabelled radiolabel radiolabeled radiolabelled undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) N/A 4067972 unspecified role unspecified role prey prey purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 4D long_ssrna oligo-rep-4 4067968 N/A 4067973 unspecified role unspecified role neutral component neutral component region radiolabelled radiolabel radiolabeled radiolabelled undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) N/A 4067972 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 4D rep-rep-210 4067969 N/A 4067972 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 N/A 4067971 unspecified role unspecified role neutral component neutral component purified purified Stoichiometry: 2.0 direct interaction direct interaction false false false Table S1 Crystals of Nsp7/8A (PDB: 6WIQ) were shown to have a truncated N-terminus (at residue Glu78) for Nsp8. For entries B/C (6WQD and 6XIP) NSP8 also starts at Asp78 because of the truncation by protease V8/Glu-C. 31mer_hairpin_rna-rep-1 4067970 N/A 4067975 enzyme enzyme neutral component neutral component purified purified ecoli Escherichia coli (strain K12) N/A 4067971 ancillary ancillary neutral component neutral component purified purified ecoli Escherichia coli (strain K12) N/A 4067976 enzyme target enzyme target substrate substrate neutral component neutral component region 32p radiolabel 32p radiolabel P32 32P 32P P32 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false in vitro In vitro N/A 4067972 ancillary ancillary neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Supp. figure 1 EDTA;CHEBI:42191 The RTC creating duplexed 36 basepaired RNA from a 31 base hairpin substrate.