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/ A dynamic regulatory interface on SARS-CoV-2 RNA polymerase A dynamic regulatory interface on SARS-CoV-2 RNA polymerase 2020 imex curation Shi W. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus This entry has been curated from a pre-print and has not been peer-reviewed. If needed, the data in this entry will be amended once the manuscript has gone through peer-review. liu00794@umn.edu,ybhu@wh.iov.cn 28-Sep-2020: Contacted by IntAct-Help. Only protein-protein interactions imex curation in vitro In vitro rna rna pol assay rna directed rna polymerase assay rna rna pol assay predetermined predetermined participant predetermined Shi W. Virus - Publications including interactions involving viral proteins This entry has been curated from a pre-print and has not been peer-reviewed. If needed, the data in this entry will be amended once the manuscript has gone through peer-review. I do not know if mutations on a complex are OK to add now; I have added them anyway, and it seemed to work. liu00794@umn.edu,ybhu@wh.iov.cn Accepted 2020-AUG-17 AT 10:21 BST AT 10:21 BST by KALPANAP 2020 imex curation A dynamic regulatory interface on SARS-CoV-2 RNA polymerase A dynamic regulatory interface on SARS-CoV-2 RNA polymerase 2020 imex curation Shi W. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus This entry has been curated from a pre-print and has not been peer-reviewed. If needed, the data in this entry will be amended once the manuscript has gone through peer-review. liu00794@umn.edu,ybhu@wh.iov.cn 28-Sep-2020: Contacted by IntAct-Help. Only protein-protein interactions imex curation 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 Shi W. Virus - Publications including interactions involving viral proteins This entry has been curated from a pre-print and has not been peer-reviewed. If needed, the data in this entry will be amended once the manuscript has gone through peer-review. I do not know if mutations on a complex are OK to add now; I have added them anyway, and it seemed to work. liu00794@umn.edu,ybhu@wh.iov.cn Accepted 2020-AUG-17 AT 10:21 BST AT 10:21 BST by KALPANAP 2020 imex curation Mock publication and experiment for abstract interactions that are not interaction evidences. Mock publication and experiment for abstract interactions that are not interaction evidences. unspecified method A dynamic regulatory interface on SARS-CoV-2 RNA polymerase A dynamic regulatory interface on SARS-CoV-2 RNA polymerase 2020 imex curation Shi W. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus This entry has been curated from a pre-print and has not been peer-reviewed. If needed, the data in this entry will be amended once the manuscript has gone through peer-review. liu00794@umn.edu,ybhu@wh.iov.cn 28-Sep-2020: Contacted by IntAct-Help. Only protein-protein interactions imex curation in vitro In vitro emsa electrophoretic mobility shift assay Gel retardation assay band shift band shift Gel retardation assay emsa predetermined predetermined participant predetermined Shi W. Virus - Publications including interactions involving viral proteins This entry has been curated from a pre-print and has not been peer-reviewed. If needed, the data in this entry will be amended once the manuscript has gone through peer-review. I do not know if mutations on a complex are OK to add now; I have added them anyway, and it seemed to work. liu00794@umn.edu,ybhu@wh.iov.cn Accepted 2020-AUG-17 AT 10:21 BST AT 10:21 BST by KALPANAP 2020 imex curation A dynamic regulatory interface on SARS-CoV-2 RNA polymerase A dynamic regulatory interface on SARS-CoV-2 RNA polymerase 2020 imex curation Shi W. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus This entry has been curated from a pre-print and has not been peer-reviewed. If needed, the data in this entry will be amended once the manuscript has gone through peer-review. liu00794@umn.edu,ybhu@wh.iov.cn 28-Sep-2020: Contacted by IntAct-Help. Only protein-protein interactions imex curation in vitro In vitro 3d-em-single electron microscopy 3D single particle reconstruction 3D-EM-single structure determination identification by structure determination identification by structure determination structure determination Shi W. Virus - Publications including interactions involving viral proteins This entry has been curated from a pre-print and has not been peer-reviewed. If needed, the data in this entry will be amended once the manuscript has gone through peer-review. liu00794@umn.edu,ybhu@wh.iov.cn Accepted 2020-AUG-17 AT 10:21 BST AT 10:21 BST by KALPANAP 2020 imex curation 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 rna primer2_gccgcc ds rna ds rna double stranded ribonucleic acid synthetic construct synthetic construct GCCGCC 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 primer1_gcuaugugagauuaaguuau RNA Primer1 ds rna ds rna double stranded ribonucleic acid synthetic construct synthetic construct GCUAUGUGAGAUUAAGUUAU rna template2_aaaaacccuuggcggc ds rna ds rna double stranded ribonucleic acid synthetic construct synthetic construct AAAAACCCUUGGCGGC 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 duplex_rna_gugggccca ds rna ds rna double stranded ribonucleic acid synthetic construct synthetic construct GUGGGCCCA rna template1_uuuuuuuuuuauaacuuaaucucacauagc RNA Template1 nucleic acid nucleic acid synthetic construct synthetic construct UUUUUUUUUUAUAACUUAAUCUCACAUAGC rep-rep-113 5 12 unspecified role unspecified role neutral component neutral component synthetic construct synthetic construct 8 unspecified role unspecified role neutral component neutral component purified purified C-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range ecoli Escherichia coli (strain K12) 6 unspecified role unspecified role neutral component neutral component purified purified C-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range ecoli Escherichia coli (strain K12) 11 unspecified role unspecified role neutral component neutral component purified purified C-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range ecoli Escherichia coli (strain K12) physical association physical association Table S1 duplex_rna_gugggccca-rep-1 1 13 enzyme target enzyme target substrate substrate 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 synthetic construct synthetic construct 26 enzyme enzyme neutral component neutral component purified purified C-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range 28 C-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range 30 C-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range 32 P0DTD1-PRO_0000449625:p.Lys27Ala mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain K A 28 P0DTD1-PRO_0000449626:p.Asp163Ala mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain D A 30 Wed Sep 16 10:22:27 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'P0DTD1-PRO_0000449626:Asp163Ala' P0DTD1-PRO_0000449626:p.Ala162Lys mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain A K 30 P0DTD1-PRO_0000449626:p.Ala181Asn mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain A N 30 ecoli Escherichia coli (strain K12) 9 enzyme target enzyme target substrate substrate 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 5-prime fluorescein fluorescein label fluorescein certain certain sequence position certain certain certain sequence position certain synthetic construct synthetic construct 38 24 rna elongation rna strand elongation rna elongation Figure 4 C/D nsp7_nsp8_nsp12_sars2-rna primer1_gcuaugugagauuaaguuau-1 4 13 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 synthetic construct synthetic construct 26 unspecified role unspecified role neutral component neutral component purified purified C-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range C-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range C-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range P0DTD1-PRO_0000449625:p.Lys27Ala 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 K A 28 P0DTD1-PRO_0000449626:p.Asp163Ala 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 D A 30 Wed Sep 16 09:49:38 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p0dtd1-pro_0000449626:Asp163Ala' P0DTD1-PRO_0000449626:p.Ala162Lys 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 A K 30 Fri Sep 18 21:58:29 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p0dtd1-pro_0000449626:p.Ala162Lys' P0DTD1-PRO_0000449626:p.Ala181Asn 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 A N 30 Wed Sep 16 11:03:58 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p0dtd1-pro_0000449626:p.Ala181Asn' ecoli Escherichia coli (strain K12) 9 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 5-prime fluorescein fluorescein label fluorescein certain certain sequence position certain certain certain sequence position certain synthetic construct synthetic construct 42 52 direct interaction direct interaction Figure 4 E/F, Supp. Fig 5A nsp7_nsp8_nsp12_sars2-rna primer1_gcuaugugagauuaaguuau-2 2 10 enzyme target enzyme target substrate substrate 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 synthetic construct synthetic construct 26 enzyme enzyme neutral component neutral component purified purified C-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range C-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range C-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range P0DTD1-PRO_0000449625:p.Lys27Ala mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain K A 28 P0DTD1-PRO_0000449626:p.Ala162Lys mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain A K 30 P0DTD1-PRO_0000449626:p.Ala181Asn mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain A N 30 P0DTD1-PRO_0000449626:p.Asp163Ala mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain D A 30 ecoli Escherichia coli (strain K12) 7 enzyme target enzyme target substrate substrate 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 synthetic construct synthetic construct 56 66 rna elongation rna strand elongation rna elongation Supp. Figure 5 B/C nsp7-nsp8-nsp12_sars2 SARS-CoV-2 polymerase complex NSP7:2xNSP8:NSP12 replication-transcription complex replication and transcription complex RTC central RTC C-RTC holo-RdRp complex holo-RNA-dependent RNA polymerase complex 6 enzyme enzyme nsp7_nsp8 binding region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 8 enzyme enzyme nsp7_nsp8 binding region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 6 enzyme enzyme nsp8_nsp12 binding region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 11 unspecified role unspecified role nsp8_nsp12 binding region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 68 71 70 68 69 71 70 69 physical association physical association SARS-CoV-2 SARS-CoV-2 SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 2019-nCoV stable complex stable complex physical interaction evidence used in manual assertion physical interaction evidence used in manual assertion IPI inferred from physical interaction RNA-directed 5'-3' RNA polymerase of the SARS-CoV-2 coronavirus which consists of the main polymerase protein NSP12 and a stoichiometric variant of the primase complex (CPX-5690). Extends partially double-stranded RNA templates and is probably also required for transcription initiation, though the mechanism for this has yet to be determined. Complex formation enhances dsRNA binding of the individual protomers. Heterotetramer Severe acute respiratory syndrome (SARS) [EFO:0000694]: A viral respiratory infection caused by the SARS coronavirus. It is transmitted through close person-to-person contact. It is manifested with high fever, headache, dry cough and myalgias. It may progress to pneumonia and cause death. Primase complex without polymerase has a different stoichiometry (8:8). NSP12 possesses conserved motifs involved in template binding, NTP binding, and polymerization that assume a structure resembling a cupped “right hand”. The NSP7-NSP8 heterodimer binds to the index finger loop and may facilitates the interaction of NSP12 with additional components of the RNA synthesis machinery. The second NSP8 molecule binds close to the RNA template-binding channel. Accepted 2020-APR-20 by ORCHARD coronavirus