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/ The SARS-CoV-2 protein ORF3a inhibits fusion of autophagosomes with lysosomes. The SARS-CoV-2 protein ORF3a inhibits fusion of autophagosomes with lysosomes. Cell discovery 2021 imex curation Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus The authors have stated that the species origin of Flag-RAB7, HA-SNAP29, FLAG-VAMP8 and all VPS39 constructs is Human. huihuili@scu.edu.cn,linyong@cqmu.edu.cn,lukf@scu.edu.cn Only protein-protein interactions imex curation human-hela Homo sapiens epitheloid cervix carcinoma cells Human hela Human epitheloid cervix carcinoma HeLa cells derivation: cervix; epithelial; adenocarcinoma ATCC no:CCL-2 anti tag coip anti tag coimmunoprecipitation anti tag coip ms participant Identification by mass spectrometry ms participant Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K. Coronavirus - Interactions investigated in the context of Coronavirus Virus - Publications including interactions involving viral proteins The authors have stated that the species origin of Flag-RAB7, HA-SNAP29, FLAG-VAMP8 and all VPS39 constructs is Human. huihuili@scu.edu.cn,linyong@cqmu.edu.cn,lukf@scu.edu.cn Accepted 2021-JUN-07 AT 09:04 BST AT 09:04 BST by ORCHARD Cell discovery 2021 Only protein-protein interactions imex curation imex curation The SARS-CoV-2 protein ORF3a inhibits fusion of autophagosomes with lysosomes. The SARS-CoV-2 protein ORF3a inhibits fusion of autophagosomes with lysosomes. Cell discovery 2021 imex curation Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus The authors have stated that the species origin of Flag-RAB7, HA-SNAP29, FLAG-VAMP8 and all VPS39 constructs is Human. huihuili@scu.edu.cn,linyong@cqmu.edu.cn,lukf@scu.edu.cn Only protein-protein interactions imex curation human-hela Homo sapiens epitheloid cervix carcinoma cells Human hela Human epitheloid cervix carcinoma HeLa cells derivation: cervix; epithelial; adenocarcinoma ATCC no:CCL-2 anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K. Coronavirus - Interactions investigated in the context of Coronavirus Virus - Publications including interactions involving viral proteins The authors have stated that the species origin of Flag-RAB7, HA-SNAP29, FLAG-VAMP8 and all VPS39 constructs is Human. huihuili@scu.edu.cn,linyong@cqmu.edu.cn,lukf@scu.edu.cn Accepted 2021-JUN-07 AT 09:04 BST AT 09:04 BST by ORCHARD Cell discovery 2021 Only protein-protein interactions imex curation imex curation The SARS-CoV-2 protein ORF3a inhibits fusion of autophagosomes with lysosomes. The SARS-CoV-2 protein ORF3a inhibits fusion of autophagosomes with lysosomes. Cell discovery 2021 imex curation Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus The authors have stated that the species origin of Flag-RAB7, HA-SNAP29, FLAG-VAMP8 and all VPS39 constructs is Human. huihuili@scu.edu.cn,linyong@cqmu.edu.cn,lukf@scu.edu.cn 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. anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K. Coronavirus - Interactions investigated in the context of Coronavirus Virus - Publications including interactions involving viral proteins The authors have stated that the cell line used in figure S2 was 293T. The authors have stated that the species origin of Flag-RAB7, HA-SNAP29, FLAG-VAMP8 and all VPS39 constructs is Human. huihuili@scu.edu.cn,linyong@cqmu.edu.cn,lukf@scu.edu.cn Accepted 2021-JUN-07 AT 09:04 BST AT 09:04 BST by ORCHARD Cell discovery 2021 Only protein-protein interactions imex curation imex curation The SARS-CoV-2 protein ORF3a inhibits fusion of autophagosomes with lysosomes. The SARS-CoV-2 protein ORF3a inhibits fusion of autophagosomes with lysosomes. Cell discovery 2021 imex curation Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus The authors have stated that the species origin of Flag-RAB7, HA-SNAP29, FLAG-VAMP8 and all VPS39 constructs is Human. huihuili@scu.edu.cn,linyong@cqmu.edu.cn,lukf@scu.edu.cn Only protein-protein interactions imex curation in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K., Zhang Y., Sun H., Pei R., Mao B., Zhao Z., Li H., Lin Y., Lu K. Coronavirus - Interactions investigated in the context of Coronavirus Virus - Publications including interactions involving viral proteins The authors have stated that the species origin of Flag-RAB7, HA-SNAP29, FLAG-VAMP8 and all VPS39 constructs is Human. huihuili@scu.edu.cn,linyong@cqmu.edu.cn,lukf@scu.edu.cn Accepted 2021-JUN-07 AT 09:04 BST AT 09:04 BST by ORCHARD Cell discovery 2021 Only protein-protein interactions imex curation imex curation vps39_human Vam6/Vps39-like protein KIAA0770 VPS39 VAM6 TLP TRAP1-like protein protein protein human Homo sapiens Human MHDAFEPVPILEKLPLQIDCLAAWEEWLLVGTKQGHLLLYRIRKDVVPADVASPESGSCNRFEVTLEKSNKNFSKKIQQIHVVSQFKILVSLLENNIYVHDLLTFQQITTVSKAKGASLFTCDLQHTETGEEVLRMCVAVKKKLQLYFWKDREFHELQGDFSVPDVPKSMAWCENSICVGFKRDYYLIRVDGKGSIKELFPTGKQLEPLVAPLADGKVAVGQDDLTVVLNEEGICTQKCALNWTDIPVAMEHQPPYIIAVLPRYVEIRTFEPRLLVQSIELQRPRFITSGGSNIIYVASNHFVWRLIPVPMATQIQQLLQDKQFELALQLAEMKDDSDSEKQQQIHHIKNLYAFNLFCQKRFDESMQVFAKLGTDPTHVMGLYPDLLPTDYRKQLQYPNPLPVLSGAELEKAHLALIDYLTQKRSQLVKKLNDSDHQSSTSPLMEGTPTIKSKKKLLQIIDTTLLKCYLHTNVALVAPLLRLENNHCHIEESEHVLKKAHKYSELIILYEKKGLHEKALQVLVDQSKKANSPLKGHERTVQYLQHLGTENLHLIFSYSVWVLRDFPEDGLKIFTEDLPEVESLPRDRVLGFLIENFKGLAIPYLEHIIHVWEETGSRFHNCLIQLYCEKVQGLMKEYLLSFPAGKTPVPAGEEEGELGEYRQKLLMFLEISSYYDPGRLICDFPFDGLLEERALLLGRMGKHEQALFIYVHILKDTRMAEEYCHKHYDRNKDGNKDVYLSLLRMYLSPPSIHCLGPIKLELLEPKANLQAALQVLELHHSKLDTTKALNLLPANTQINDIRIFLEKVLEENAQKKRFNQVLKNLLHAEFLRVQEERILHQQVKCIITEEKVCMVCKKKIGNSAFARYPNGVVVHYFCSKEVNPADT E5A40A3C787EB112 rab7a_human Ras-related protein Rab-7a RAB7A RAB7 protein protein human Homo sapiens Human MTSRKKVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVELYNEFPEPIKLDKNDRAKASAESCSC DIP protein P51149 original sequence version: 113 DIP protein P51149 original sequence version: 92 DIP protein P51149 original sequence version: 162 A2AF33B16A672971 vamp8_human Vesicle-associated membrane protein 8 Endobrevin VAMP8 protein protein human Homo sapiens Human MEEASEGGGNDRVRNLQSEVEGVKNIMTQNVERILARGENLEHLRNKTEDLEATSEHFKTTSQKVARKFWWKNVKMIVLICVIVFIIILFIVLFATGAFS DIP protein Q9BV40 original sequence version: 108 DIP protein Q9BV40 original sequence version: 118 DIP protein Q9BV40 original sequence version: 100 018B986442BBD9B6 snp29_human Synaptosomal-associated protein 29 Vesicle-membrane fusion protein SNAP-29 Soluble 29 kDa NSF attachment protein SNAP29 protein protein human Homo sapiens Human MSAYPKSYNPFDDDGEDEGARPAPWRDARDLPDGPDAPADRQQYLRQEVLRRAEATAASTSRSLALMYESEKVGVASSEELARQRGVLERTEKMVDKMDQDLKISQKHINSIKSVFGGLVNYFKSKPVETPPEQNGTLTSQPNNRLKEAISTSKEQEAKYQASHPNLRKLDDTDPVPRGAGSAMSTDAYPKNPHLRAYHQKIDSNLDELSMGLGRLKDIALGMQTEIEEQDDILDRLTTKVDKLDVNIKSTERKVRQL DIP protein O95721 original sequence version: 135 DIP protein O95721 original sequence version: 139 DIP protein O95721 original sequence version: 118 7E1CDBA22D6F5A3C ap3a_sars2 ORF3a protein Accessory protein 3a Protein U274 Protein X1 3a Protein 3a protein protein SARS-CoV-2 SARS-CoV-2 SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 2019-nCoV MDLFMRIFTIGTVTLKQGEIKDATPSDFVRATATIPIQASLPFGWLIVGVALLAVFQSASKIITLKKRWQLALSKGVHFVCNLLLLFVTVYSHLLLVAAGLEAPFLYLYALVYFLQSINFVRIIMRLWLCWKCRSKNPLLYDANYFLCWHTNCYDYCIPYNSVTSSIVITSGDGTTSPISEHDYQIGGYTEKWESGVKDCVVLHSYFTSDYYQLYSTQLSTDTGVEHVTFFIYNKIVDEPEEHVQIHTIDGSSGVVNPVMEPIYDEPTTTTSVPL ap3a_sars2-vps39-2 1 9 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed region gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 5 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level physical association physical association 5B ap3a_sars2-vps39-5 4 9 unspecified role unspecified role bait bait purified purified n-terminus gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range P0DTC3:p.Tyr160Ala mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain Y A ecoli Escherichia coli (strain K12) 5 unspecified role unspecified role prey prey purified purified region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined ecoli Escherichia coli (strain K12) direct interaction direct interaction 5 E/G ap3a_sars2-vps39-6 2 6 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed 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 9 inhibitor inhibitor prey prey over-expressed over expressed level over-expressed region gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 5 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association 5I Orf3a expression dramatically reduced the interaction between RAB7 and VPS39. vps39-rab7a-1 2 6 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed 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 5 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association 5I snap29-vamp8-1 2 7 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed 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 8 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association 5J ORF3a - P0DTC3. ap3a_sars2-vps39-7 3 9 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed region gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined P0DTC3:p.Tyr160Ala mutation disrupting strength mutation disrupting interaction strength mutation disrupting strength certain certain sequence position certain certain certain sequence position certain Y A 5 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association Supplementary figure 2 A/B The authors have stated that 293T was the cell line used in Figure S2.