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/ Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme. Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme. Science (New York, N.Y.) 2021 imex curation Liu C., Shi W., Becker ST., Schatz DG., Liu B., Yang Y. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus liu00794@umn.edu, yan9yang@iastate.edu Only protein-protein interactions imex curation in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Liu C., Shi W., Becker ST., Schatz DG., Liu B., Yang Y. Virus - Publications including interactions involving viral proteins liu00794@umn.edu, yan9yang@iastate.edu Accepted 2021-NOV-10 AT 09:30 GMT AT 09:30 GMT by LUANA Science (New York, N.Y.) 2021 Only protein-protein interactions imex curation imex curation Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme. Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme. Science (New York, N.Y.) 2021 imex curation Liu C., Shi W., Becker ST., Schatz DG., Liu B., Yang Y. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus liu00794@umn.edu, yan9yang@iastate.edu Only protein-protein interactions imex curation in vitro In vitro 3d-em 3D electron microscopy 3D-EM electron tomog structure determination identification by structure determination identification by structure determination structure determination Liu C., Shi W., Becker ST., Schatz DG., Liu B., Yang Y. Virus - Publications including interactions involving viral proteins liu00794@umn.edu, yan9yang@iastate.edu Accepted 2021-NOV-10 AT 09:30 GMT AT 09:30 GMT by LUANA Science (New York, N.Y.) 2021 Only protein-protein interactions imex curation 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 Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme. Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme. Science (New York, N.Y.) 2021 imex curation Liu C., Shi W., Becker ST., Schatz DG., Liu B., Yang Y. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus liu00794@umn.edu, yan9yang@iastate.edu Only protein-protein interactions imex curation in vitro In vitro cleavage cleavage assay cleavage weight by sybr molecular weight estimation by sybr staining safe DNA gel stain safe DNA gel stain weight by sybr Liu C., Shi W., Becker ST., Schatz DG., Liu B., Yang Y. Virus - Publications including interactions involving viral proteins liu00794@umn.edu, yan9yang@iastate.edu Accepted 2021-NOV-10 AT 09:30 GMT AT 09:30 GMT by LUANA Science (New York, N.Y.) 2021 Only protein-protein interactions imex curation 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 p0dtd1-pro_0000449628 Non-structural protein 10 rep ORF1ab polyprotein 1a-1b protein protein SARS-CoV-2 SARS-CoV-2 SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 2019-nCoV AGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQ 4254 4392 p32-1 rna ribonucleic acid RNA rna in vitro In vitro GGUCAUUCUCCUAAGAAGCUAUUAAAAUCACC p0dtd1-pro_0000449631 Proofreading exoribonuclease nsp14 rep ORF1ab polyprotein 1a-1b protein protein SARS-CoV-2 SARS-CoV-2 SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 2019-nCoV AENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQ 5926 6452 t45 rna ribonucleic acid RNA rna in vitro In vitro CCAGUAAGAGGAUUCUUCGAUAAUUUUAGUGUACCCCUAUCGUGA t35p31 ds rna ds rna double stranded ribonucleic acid in vitro In vitro GGGGAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGACUUCGGUCAUUCUCCUAAGAAGCUAUUAAAAUCACC residues 29839-29870 from NC_045512.2 (3' region minus polyA tail) rep-rep-259 2 10 unspecified role unspecified role neutral component neutral component 5' prime Guanosine rna chemical modification RNA chemical modification RNA chemical modification post-transcriptional modification rna chemical modification certain certain sequence position certain certain certain sequence position certain 2'-O-methyl rna chemical modification RNA chemical modification RNA chemical modification post-transcriptional modification rna chemical modification certain certain sequence position certain certain certain sequence position certain in vitro In vitro 16 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 18 ecoli Escherichia coli (strain K12) direct interaction direct interaction Table S1 PDBe entries 7n0b and 7n0d appear to have 4 rather than the stated 3 guanine residues at the 5' terminus of the T-strand RNA;the authors state that "5'-end non-templated nucleotide addition by T7 RNAP has been observed when there are multiple initiating guanosines in the RNA transcript". rep-rep-260 2 10 unspecified role unspecified role neutral component neutral component 5' prime Guanosine rna chemical modification RNA chemical modification RNA chemical modification post-transcriptional modification rna chemical modification certain certain sequence position certain certain certain sequence position certain 2'-O-methyl rna chemical modification RNA chemical modification RNA chemical modification post-transcriptional modification rna chemical modification certain certain sequence position certain certain certain sequence position certain in vitro In vitro 16 unspecified role unspecified role neutral component neutral component purified purified P0DTD1-PRO_0000449631:p.Glu191Ala mutation mutation certain certain sequence position certain certain certain sequence position certain E A 18 Tue Oct 05 19:26:51 BST 2021 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Glu191Ala' 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 18 ecoli Escherichia coli (strain K12) direct interaction direct interaction Table S1 PDBe entries 7n0b and 7n0d appear to have 4 rather than the stated 3 guanine residues at the 5' terminus of the T-strand RNA;the authors state that "5'-end non-templated nucleotide addition by T7 RNAP has been observed when there are multiple initiating guanosines in the RNA transcript". I have NOT added the CCCCC chain in 7n0d entry as text only states - "...the cryo-EM map shows well-resolved densities for five consecutive pyrimidine nucleotides in the substrate-binding pockets of protomers B and D. Therefore, five CMP residues were built in the map to form four C-G base pairs with the 5' overhang of T35P31 RNA" so is it really present ? -pyrimidines can be Thymine as well. The "P" strand in the 7n0d PDBe entry has a different 5' sequence to that in entry 7n0b and 7n0c. The same sequence as in entries 7n0b and 7n0c has been used here. Entry 7n0d refers to a higher order oligomer. [Entry 7n0d shows well-resolved densities for five consecutive pyrimidine nucleotides in the substrate-binding pockets of protomers B and D;the exact source and identify of the second RNA substrate molecule are unclear.] rep-rep-261 4 10 enzyme target enzyme target substrate substrate neutral component neutral component 2'-O-methyl rna chemical modification RNA chemical modification RNA chemical modification post-transcriptional modification rna chemical modification certain certain sequence position certain certain certain sequence position certain in vitro In vitro 8 enzyme enzyme neutral component neutral component purified purified P0DTD1-PRO_0000449631:p.Glu191Ala mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain E A Tue Oct 05 19:27:37 BST 2021 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Glu191Ala' 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) 6 ancillary ancillary neutral component neutral component purified purified ecoli Escherichia coli (strain K12) cleavage cleavage reaction cleavage 1B not entered the complex as Roles cannot be assigned. MgCl2 (CHEBI:6636 ) CaCl2 (CHEBI:3312) rep-rep-262 2 10 unspecified role unspecified role neutral component neutral component 2'-O-methyl rna chemical modification RNA chemical modification RNA chemical modification post-transcriptional modification rna chemical modification certain certain sequence position certain certain certain sequence position certain in vitro In vitro 16 unspecified role unspecified role neutral component neutral component purified purified P0DTD1-PRO_0000449631:p.Glu191Ala mutation mutation certain certain sequence position certain certain certain sequence position certain E A 18 Tue Oct 05 18:55:33 BST 2021 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Glu191Ala' 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 18 ecoli Escherichia coli (strain K12) direct interaction direct interaction Table S1 The "P" strand in the 7n0d PDBe entry has a different 5' sequence to that in entry 7n0b and 7n0c. The same sequence as in entries 7n0b and 7n0c has been used here. rep-rep-263 4 7 enzyme target enzyme target substrate substrate neutral component neutral component 2'-O-methyl-CMP 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 3'-dCMP mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain 2'-dCMP mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain in vitro In vitro 8 enzyme enzyme neutral component neutral component purified purified P0DTD1-PRO_0000449631:p.Glu191Ala mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain E A Tue Oct 05 19:01:45 BST 2021 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Glu191Ala' 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) 6 ancillary ancillary neutral component neutral component purified purified ecoli Escherichia coli (strain K12) cleavage cleavage reaction cleavage 4B rep-rep-264 1 5 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) 16 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 18 ecoli Escherichia coli (strain K12) physical association physical association Supp. figure 1A,2A nsp8 co-eluted with the nsp10-nsp14-RNA complex on the SEC column:association of nsp8 with the nsp10-nsp14-RNA complex is weak. rep-rep-265 4 5 stimulator stimulator neutral component neutral component purified purified ecoli Escherichia coli (strain K12) 10 enzyme target enzyme target substrate substrate neutral component neutral component 2'-O-methyl rna chemical modification RNA chemical modification RNA chemical modification post-transcriptional modification rna chemical modification certain certain sequence position certain certain certain sequence position certain in vitro In vitro 8 enzyme enzyme 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) 6 ancillary ancillary neutral component neutral component purified purified ecoli Escherichia coli (strain K12) cleavage cleavage reaction cleavage S5B not entered the complex as Roles cannot be assigned. p32_1-rep-1 4 9 enzyme target enzyme target substrate substrate neutral component neutral component whole molecule sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain 3-prime biotin tag biotin tag certain certain sequence position certain certain certain sequence position certain in vitro In vitro 7 enzyme target enzyme target substrate substrate neutral component neutral component whole molecule sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain in vitro In vitro 8 enzyme enzyme neutral component neutral component purified purified P0DTD1-PRO_0000449631:p.Glu191Ala mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain E A Tue Oct 05 19:10:26 BST 2021 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Glu191Ala' 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) 6 ancillary ancillary neutral component neutral component purified purified ecoli Escherichia coli (strain K12) 65 62 cleavage cleavage reaction cleavage Supp. figure 9 It is stated that "T45 corresponds to the 3'-end 44 nt of SARS-CoV-2 genome followed by a CMP";however even after removing several residues from both 3' and 5' sequences, no match to any SARS2 sequence was found on Blasting. I would expect the 3' end to be at residue 45- but they have printed it the other way around and I had enough trouble copying it from the figure without trying to reverse it - please feel free to alter if you wish. There does not appear to be a tool to do this. (?) nsp10-nsp14_sars2-1 SARS-CoV-2 3'-5' exoribonuclease proof-reading complex NSP10:NSP14 SARS-CoV-2 NSP14/NSP10 complex 8 enzyme enzyme nsp10 binding region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 6 unspecified role unspecified role nsp14 binding region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 70 72 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 The SARS-CoV-2 coronavirus 3'-5' exoribonuclease complex which strictly targets double-stranded RNA and can selectively remove a mismatched ribonucleotide at the 3'-end of a dsRNA substrate. Formation of the NSP10-NSP14 complex strongly enhances the exonuclease activity of the bifunctional NSP14 and enhances the fidelity of RNA synthesis by correcting nucleotide incorporation errors made by the RNA-dependent RNA polymerase. May bind to, and act with the nsp7/nsp8/nsp12 polymerase complex (CPX-5742). Proof-reading exonuclease activity may explain why coronaviruses have the largest RNA genomes known to date. Complex formation does not appear to effect the C-terminal N7-methyltransferase activity of NSP14 involved in RNA cap modification. 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. NSP10 forms a homododecamer in isolation. A flexible N-terminal domain of NSP14 forms the NSP10 docking site and induces conformational changes in the NSP14 that modulate the distance between the catalytic residues. New version remark: PMID:29279395 describes nsp14 as a 3'-5'-exoribonuclease. See also review PMID:31440227. Description, properties and xrefs updated and GO added as per Sandra's addition on SARS-CoV entry EBI-25496027/CPX-5707. Also updated this entry to "by orthology" as SARS-CoV has exp-evidence. Accepted 2020-APR-20 by ORCHARD coronavirus