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/ ORF10-Cullin-2-ZYG11B complex is not required for SARS-CoV-2 infection. ORF10-Cullin-2-ZYG11B complex is not required for SARS-CoV-2 infection. Proceedings of the National Academy of Sciences of the United States of America 2021 imex curation Mena EL., Donahue CJ., Vaites LP., Li J., Rona G., O'Leary C., Lignitto L., Miwatani-Minter B., Paulo JA., Dhabaria A., Ueberheide B., Gygi SP., Pagano M., Harper JW., Davey RA., Elledge SJ. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus SARS-CoV-2 genome annotation reveals 10 ORFs, of which the last one (ORF10) is positioned downstream of the N gene. It is a hypothetical, 117 nt—long ORF, which was speculated to encode a 38 aa protein. There is growing evidence that the ORF10 is not a coding region;the evidence for the presence of the subgenomic mRNAs corresponding to ORF10 is limited. The MS data in Tables 1+2 is full of Crapome proteins, and there are some in figure 1 as well. Although SAINT scores are meant to be experiment specific, I have been told - in the past- by MS/Pride persons that any score below 0.9 is of rather low confidence. Orf10 has been entered as Uniprot (Trembl) A0A663DJA2 as taken from pmid:32353859 (Gordon et al.) and Addgene website (Ref_seq YP_009725255.1). Michele.Pagano@nyulangone.org,wade_harper@hms.harvard.edu,radavey@bu.edu,selledge@genetics.med.harvard.edu. Only protein-protein interactions imex curation human-293t Homo sapiens 293 cells transformed with SV40 large T antigen 293t 293 cells expressing SV40 large T antigen. The original designation of this cell line was 293tsA1609neo. It is not in Cabri,ATCC or HyperCLDB. pull down pull down sequence tag sequence tag identification sequence tag Mena EL., Donahue CJ., Vaites LP., Li J., Rona G., O'Leary C., Lignitto L., Miwatani-Minter B., Paulo JA., Dhabaria A., Ueberheide B., Gygi SP., Pagano M., Harper JW., Davey RA., Elledge SJ. Virus - Publications including interactions involving viral proteins Results obtained using ORF10−2xStrep expressed from a pcDNA3 vector, have not been included as the SAINT scores are too low. Using the LVX vector only proteins with a SAINT score of ~>0.9 have been included. SARS-CoV-2 genome annotation reveals 10 ORFs, of which the last one (ORF10) is positioned downstream of the N gene. It is a hypothetical, 117 nt—long ORF, which was speculated to encode a 38 aa protein. There is growing evidence that the ORF10 is not a coding region;the evidence for the presence of the subgenomic mRNAs corresponding to ORF10 is limited. The MS data in Tables 1+2 is full of Crapome proteins, and there are some in figure 1 as well. Although SAINT scores are meant to be experiment specific, I have been told - in the past- by MS/Pride persons that any score below 0.9 is of rather low confidence. Orf10 has been entered as Uniprot (Trembl) A0A663DJA2 as taken from pmid:32353859 (Gordon et al.) and Addgene website (Ref_seq YP_009725255.1). Michele.Pagano@nyulangone.org,wade_harper@hms.harvard.edu,radavey@bu.edu,selledge@genetics.med.harvard.edu. Accepted 2021-JUL-05 AT 07:24 BST AT 07:24 BST by KALPANAP Proceedings of the National Academy of Sciences of the United States of America 2021 Only protein-protein interactions imex curation imex curation ORF10-Cullin-2-ZYG11B complex is not required for SARS-CoV-2 infection. ORF10-Cullin-2-ZYG11B complex is not required for SARS-CoV-2 infection. Proceedings of the National Academy of Sciences of the United States of America 2021 imex curation Mena EL., Donahue CJ., Vaites LP., Li J., Rona G., O'Leary C., Lignitto L., Miwatani-Minter B., Paulo JA., Dhabaria A., Ueberheide B., Gygi SP., Pagano M., Harper JW., Davey RA., Elledge SJ. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus SARS-CoV-2 genome annotation reveals 10 ORFs, of which the last one (ORF10) is positioned downstream of the N gene. It is a hypothetical, 117 nt—long ORF, which was speculated to encode a 38 aa protein. There is growing evidence that the ORF10 is not a coding region;the evidence for the presence of the subgenomic mRNAs corresponding to ORF10 is limited. The MS data in Tables 1+2 is full of Crapome proteins, and there are some in figure 1 as well. Although SAINT scores are meant to be experiment specific, I have been told - in the past- by MS/Pride persons that any score below 0.9 is of rather low confidence. Orf10 has been entered as Uniprot (Trembl) A0A663DJA2 as taken from pmid:32353859 (Gordon et al.) and Addgene website (Ref_seq YP_009725255.1). Michele.Pagano@nyulangone.org,wade_harper@hms.harvard.edu,radavey@bu.edu,selledge@genetics.med.harvard.edu. Only protein-protein interactions imex curation human-293t Homo sapiens 293 cells transformed with SV40 large T antigen 293t 293 cells expressing SV40 large T antigen. The original designation of this cell line was 293tsA1609neo. It is not in Cabri,ATCC or HyperCLDB. pull down pull down western blot western blot Immuno blot Immuno blot Mena EL., Donahue CJ., Vaites LP., Li J., Rona G., O'Leary C., Lignitto L., Miwatani-Minter B., Paulo JA., Dhabaria A., Ueberheide B., Gygi SP., Pagano M., Harper JW., Davey RA., Elledge SJ. Virus - Publications including interactions involving viral proteins Results obtained using ORF10−2xStrep expressed from a pcDNA3 vector, have not been included as the SAINT scores are too low. Using the LVX vector only proteins with a SAINT score of ~>0.9 have been included. SARS-CoV-2 genome annotation reveals 10 ORFs, of which the last one (ORF10) is positioned downstream of the N gene. It is a hypothetical, 117 nt—long ORF, which was speculated to encode a 38 aa protein. There is growing evidence that the ORF10 is not a coding region;the evidence for the presence of the subgenomic mRNAs corresponding to ORF10 is limited. The MS data in Tables 1+2 is full of Crapome proteins, and there are some in figure 1 as well. Although SAINT scores are meant to be experiment specific, I have been told - in the past- by MS/Pride persons that any score below 0.9 is of rather low confidence. Orf10 has been entered as Uniprot (Trembl) A0A663DJA2 as taken from pmid:32353859 (Gordon et al.) and Addgene website (Ref_seq YP_009725255.1). Michele.Pagano@nyulangone.org,wade_harper@hms.harvard.edu,radavey@bu.edu,selledge@genetics.med.harvard.edu. Accepted 2021-JUL-05 AT 07:24 BST AT 07:24 BST by KALPANAP Proceedings of the National Academy of Sciences of the United States of America 2021 Only protein-protein interactions imex curation imex curation cul2_human Cullin-2 CUL2 protein protein human Homo sapiens Human MSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTETKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNKLTEADLQYGYGGVDMNEPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGEDPNQKVIHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVLGRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVLLRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNGDQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFITVFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDMSVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADEYSYVA DIP protein Q13617 original sequence version: 129 DIP protein Q13617 original sequence version: 127 DIP protein Q13617-1 original sequence version: 139 DIP protein Q13617 original sequence version: 111 DIP protein Q13617 original sequence version: 102 30647248F671AB0E zy11b_human Protein zyg-11 homolog B ZYG11B KIAA1730 protein protein human Homo sapiens Human MPEDQAGAAMEEASPYSLLDICLNFLTTHLEKFCSARQDGTLCLQEPGVFPQEVADRLLRTMAFHGLLNDGTVGIFRGNQMRLKRACIRKAKISAVAFRKAFCHHKLVELDATGVNADITITDIISGLGSNKWIQQNLQCLVLNSLTLSLEDPYERCFSRLSGLRALSITNVLFYNEDLAEVASLPRLESLDISNTSITDITALLACKDRLKSLTMHHLKCLKMTTTQILDVVRELKHLNHLDISDDKQFTSDIALRLLEQKDILPNLVSLDVSGRKHVTDKAVEAFIQQRPSMQFVGLLATDAGYSEFLTGEGHLKVSGEANETQIAEALKRYSERAFFVREALFHLFSLTHVMEKTKPEILKLVVTGMRNHPMNLPVQLAASACVFNLTKQDLAAGMPVRLLADVTHLLLKAMEHFPNHQQLQKNCLLSLCSDRILQDVPFNRFEAAKLVMQWLCNHEDQNMQRMAVAIISILAAKLSTEQTAQLGTELFIVRQLLQIVKQKTNQNSVDTTLKFTLSALWNLTDESPTTCRHFIENQGLELFMRVLESFPTESSIQQKVLGLLNNIAEVQELHSELMWKDFIDHISSLLHSVEVEVSYFAAGIIAHLISRGEQAWTLSRSQRNSLLDDLHSAILKWPTPECEMVAYRSFNPFFPLLGCFTTPGVQLWAVWAMQHVCSKNPSRYCSMLIEEGGLQHLYNIKDHEHTDPHVQQIAVAILDSLEKHIVRHGRPPPCKKQPQARLN 0D8C19251CA67573 bip_human Endoplasmic reticulum chaperone BiP HSPA5 GRP78 Immunoglobulin heavy chain-binding protein 78 kDa glucose-regulated protein Binding-immunoglobulin protein Heat shock protein 70 family protein 5 Heat shock protein family A member 5 protein protein human Homo sapiens Human MKLSLVAAMLLLLSAARAEEEDKKEDVGTVVGIDLGTTYSCVGVFKNGRVEIIANDQGNRITPSYVAFTPEGERLIGDAAKNQLTSNPENTVFDAKRLIGRTWNDPSVQQDIKFLPFKVVEKKTKPYIQVDIGGGQTKTFAPEEISAMVLTKMKETAEAYLGKKVTHAVVTVPAYFNDAQRQATKDAGTIAGLNVMRIINEPTAAAIAYGLDKREGEKNILVFDLGGGTFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGKDVRKDNRAVQKLRREVEKAKRALSSQHQARIEIESFYEGEDFSETLTRAKFEELNMDLFRSTMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVKEFFNGKEPSRGINPDEAVAYGAAVQAGVLSGDQDTGDLVLLDVCPLTLGIETVGGVMTKLIPRNTVVPTKKSQIFSTASDNQPTVTIKVYEGERPLTKDNHLLGTFDLTGIPPAPRGVPQIEVTFEIDVNGILRVTAEDKGTGNKNKITITNDQNRLTPEEIERMVNDAEKFAEEDKKLKERIDTRNELESYAYSLKNQIGDKEKLGGKLSSEDKETMEKAVEEKIEWLESHQDADIEDFKAKKKELEEIVQPIISKLYGSAGPPPTGEEDTAEKDEL DIP protein P11021 original sequence version: 127 DIP protein P11021 original sequence version: 137 DIP protein P11021 original sequence version: 185 59B7D8D85BC32A00 calx_human Calnexin CANX Major histocompatibility complex class I antigen-binding protein p88 p90 IP90 protein protein human Homo sapiens Human MEGKWLLCMLLVLGTAIVEAHDGHDDDVIDIEDDLDDVIEEVEDSKPDTTAPPSSPKVTYKAPVPTGEVYFADSFDRGTLSGWILSKAKKDDTDDEIAKYDGKWEVEEMKESKLPGDKGLVLMSRAKHHAISAKLNKPFLFDTKPLIVQYEVNFQNGIECGGAYVKLLSKTPELNLDQFHDKTPYTIMFGPDKCGEDYKLHFIFRHKNPKTGIYEEKHAKRPDADLKTYFTDKKTHLYTLILNPDNSFEILVDQSVVNSGNLLNDMTPPVNPSREIEDPEDRKPEDWDERPKIPDPEAVKPDDWDEDAPAKIPDEEATKPEGWLDDEPEYVPDPDAEKPEDWDEDMDGEWEAPQIANPRCESAPGCGVWQRPVIDNPNYKGKWKPPMIDNPSYQGIWKPRKIPNPDFFEDLEPFRMTPFSAIGLELWSMTSDIFFDNFIICADRRIVDDWANDGWGLKKAADGAAEPGVVGQMIEAAEERPWLWVVYILTVALPVFLVILFCCSGKKQTSGMEYKKTDAPQPDVKEEEEEKEEEKDKGDEEEEGEEKLEEKQKSDAEEDGGTVSQEEEDRKPKAEEDEILNRSPRNRKPRRE DIP protein P27824 original sequence version: 177 EDE094D9B82261EE eloc_human Elongin-C ELOC Elongin 15 kDa subunit RNA polymerase II transcription factor SIII subunit C SIII p15 TCEB1 Transcription elongation factor B polypeptide 1 protein protein human Homo sapiens Human MDGEEKTYGGCEGPDAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC 98D88696E883538B elob_human Elongin-B ELOB Elongin 18 kDa subunit RNA polymerase II transcription factor SIII subunit B SIII p18 TCEB2 Transcription elongation factor B polypeptide 2 protein protein human Homo sapiens Human MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ C045F58FBED0EC47 a0a663dja2_sars2 ORF10 orf10 protein protein SARS-CoV-2 SARS-CoV-2 SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 2019-nCoV MGYINVFAFPFTIYSLLLCRMNSRNYIAQVDVVNFNLT fen1_human Flap endonuclease 1 Flap structure-specific endonuclease 1 Maturation factor 1 DNase IV FEN1 RAD2 protein protein human Homo sapiens Human MGIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTQGRLDDFFKVTGSLSSAKRKEPEPKGSTKKKAKTGAAGKFKRGK DIP protein P39748 original sequence version: 106 DIP protein P39748 original sequence version: 112 DIP protein P39748 original sequence version: 160 5154F2F6E57592C5 amy2b_human Alpha-amylase 2B 1,4-alpha-D-glucan glucanohydrolase 2B Carcinoid alpha-amylase AMY2B protein protein human Homo sapiens Human MKFFLLLFTIGFCWAQYSPNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIHNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMSGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLVGLLDLALEKDYVRSKIAEYMNHLIDIGVAGFRLDASKHMWPGDIKAILDKLHNLNSNWFPAGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRQFQNGNDVNDWVGPPNNNGVIKEVTINPDTTCGNDWVCEHRWRQIRNMVNFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWTFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL 05FC3B1EC1143857 orf10-amy2b-1 1 4 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 6 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 11 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 7 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 10 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 5 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 9 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed 2xstrep tag plus short linker strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range association association 1 B/D orf10-canx-1 2 4 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 3 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 8 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level 9 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed 2xstrep tag plus short linker strep tag strep tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range A0A663DJA2:p.Gly2Ser mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain G S Mon Jun 28 16:50:40 BST 2021 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Gly2Ser' association association 1 E