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/ liu-2010-39 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 J., Wu P., Gao F., Qi J., Kawana-Tachikawa A., Xie J., Vavricka CJ., Iwamoto A., Li T., Gao GF. Coronavirus - Interactions investigated in the context of Coronavirus gaof@im.ac.cn,litsh@263.net Journal of virology 2010 Only protein-protein interactions imex curation imex curation liu-2010-38 in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Liu J., Wu P., Gao F., Qi J., Kawana-Tachikawa A., Xie J., Vavricka CJ., Iwamoto A., Li T., Gao GF. Coronavirus - Interactions investigated in the context of Coronavirus gaof@im.ac.cn,litsh@263.net Journal of virology 2010 Only protein-protein interactions imex curation imex curation nef_hv1a2 Protein Nef nef Negative factor 3'ORF protein protein hv1a2 Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2) MGGKWSKRSMGGWSAIRERMRRAEPRAEPAADGVGAVSRDLEKHGAITSSNTAATNADCAWLEAQEEEEVGFPVRPQVPLRPMTYKAALDISHFLKEKGGLEGLIWSQRRQEILDLWIYHTQGYFPDWQNYTPGPGIRYPLTFGWCFKLVPVEPEKVEEANEGENNSLLHPMSLHGMEDAEKEVLVWRFDSKLAFHHMARELHPEYYKDC Down-modulates surface MHC-I molecules. Internalized molecules are sequestred to the trans-Golgi network (TGN). Also decreases cell surface CD4 antigen by interacting with the Src family kinase LCK thereby inducing LCK-CD4 dissociation and by increasing clathrin-dependent endocytosis of this antigen to target it to lysosomal degradation. Peroxisomal acyl-coenzyme A thioester hydrolase 1 (PTE1) seems to be involved in this process. May serve as a direct bridge between CD4 and the cellular endocytic machinery by interacting with beta-COP and adaptins. In consequence, surface MHC-I and CD4 are decreased and infected cells are masked for immune recognition by cytotoxic T lymphocytes. Decreasing the number of viral receptors prevents reinfection by more HIV particles Bypasses host T-cell signaling by inducing a transcriptional program nearly identical to that of anti-CD3 cell activation. Interacts with the TCR-zeta chain to up-regulate the Fas ligand (FasL). Increasing surface FasL molecules and decreasing surface MHC-I molecules send attacking cytotoxic T-cell into apoptosis Protects the infected cell from apoptosis in order to keep it alive until the next virus generation is ready to strike. Inhibits the Fas and TNFR-mediated death signals by blocking MAP3K5. Interacts with p53 and decreases the half-life of the latter, protecting the infected cell against p53-mediated apoptosis. Inhibits the apoptotic signals regulated by the Bcl-2 family proteins through the formation of a Nef/PI3-kinase/PAK2 complex that induces phosphorylation of Bad mint homomint Early protein that seems to play a role in optimizing the host cell environment for viral replication without causing cell death by apoptosis. Enhances virus infectivity and pathogenicity hlaa_human HLA class I histocompatibility antigen, A alpha chain HLA-A HLAA Human leukocyte antigen A protein protein human Homo sapiens Human MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDQETRNVKAQSQTDRVDLGTLRGYYNQSEAGSHTIQIMYGCDVGSDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAAHEAEQLRAYLDGTCVEWLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWELSSQPTIPIVGIIAGLVLLGAVITGAVVAAVMWRRKSSDRKGGSYTQAASSDSAQGSDVSLTACKV b2mg_human Beta-2-microglobulin B2M CDABP0092 HDCMA22P protein protein human Homo sapiens Human MSRSVALAVLALLSLSGLEAIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM ncap_sars Nucleoprotein N 9a Nucleocapsid protein protein protein sars-cov Human SARS coronavirus SARS-CoV Severe acute respiratory syndrome coronavirus MSDNGPQSNQRSAPRITFGGPTDSTDNNQNGGRNGARPKQRRPQGLPNNTASWFTALTQHGKEELRFPRGQGVPINTNSGPDDQIGYYRRATRRVRGGDGKMKELSPRWYFYYLGTGPEASLPYGANKEGIVWVATEGALNTPKDHIGTRNPNNNAATVLQLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRGNSRNSTPGSSRGNSPARMASGGGETALALLLLDRLNQLESKVSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKQYNVTQAFGRRGPEQTQGNFGDQDLIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYHGAIKLDDKDPQFKDNVILLNKHIDAYKTFPPTEPKKDKKKKTDEAQPLPQRQKKQPTVTLLPAADMDDFSRQLQNSMSGASADSTQA mint Major structural component of virions that associates with genomic RNA to form a long, flexible, helical nucleocapsid b2m-hla_a-8 3678197 N/A 3678199 unspecified role unspecified role neutral component neutral component Nef138-10 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 3678200 unspecified role unspecified role neutral component neutral component purified purified partial_ecd sufficient to bind sufficient binding region sufficient to bind range range range range false p.Phe33Ser variant variant certain certain sequence position certain certain certain sequence position certain false p.Gln86Glu variant variant certain certain sequence position certain certain certain sequence position certain false p.Arg89_Asn90delinsGlyLys variant variant certain certain sequence position certain certain certain sequence position certain false p.Gln94His variant variant certain certain sequence position certain certain certain sequence position certain false p.Val100_Asp101delinsGluAsn variant variant certain certain sequence position certain certain certain sequence position certain false p.Gly103_Gly107delinsArgIleAlaLeuArg variant variant certain certain sequence position certain certain certain sequence position certain false p.Ile119Leu variant variant certain certain sequence position certain certain certain sequence position certain false p.Ile121Met variant variant certain certain sequence position certain certain certain sequence position certain false p.Tyr123Phe variant variant certain certain sequence position certain certain certain sequence position certain false p.Arg138His variant variant certain certain sequence position certain certain certain sequence position certain false p.Asp140Tyr variant variant certain certain sequence position certain certain certain sequence position certain false p.Asn151Lys variant variant certain certain sequence position certain certain certain sequence position certain false p.Glu176Val variant variant certain certain sequence position certain certain certain sequence position certain false p.Leu180Gln variant variant certain certain sequence position certain certain certain sequence position certain false p.Asp185Glu variant variant certain certain sequence position certain certain certain sequence position certain false p.Glu190_Trp191delinsAspGly variant variant certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3678201 unspecified role unspecified role neutral component neutral component purified purified region sufficient to bind sufficient binding region sufficient to bind range range range range false ecoli Escherichia coli (strain K12) physical association physical association false false false 2 In the absence of peptide there is no interaction. HLA-A*2402 b2m-hla_a-9 3678197 N/A 3678202 unspecified role unspecified role neutral component neutral component N1 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 3678200 unspecified role unspecified role neutral component neutral component purified purified partial_ecd sufficient to bind sufficient binding region sufficient to bind range range range range false p.Phe33Ser variant variant certain certain sequence position certain certain certain sequence position certain false p.Gln86Glu variant variant certain certain sequence position certain certain certain sequence position certain false p.Arg89_Asn90delinsGlyLys variant variant certain certain sequence position certain certain certain sequence position certain false p.Gln94His variant variant certain certain sequence position certain certain certain sequence position certain false p.Val100_Asp101delinsGluAsn variant variant certain certain sequence position certain certain certain sequence position certain false p.Gly103_Gly107delinsArgIleAlaLeuArg variant variant certain certain sequence position certain certain certain sequence position certain false p.Ile119Leu variant variant certain certain sequence position certain certain certain sequence position certain false p.Ile121Met variant variant certain certain sequence position certain certain certain sequence position certain false p.Tyr123Phe variant variant certain certain sequence position certain certain certain sequence position certain false p.Arg138His variant variant certain certain sequence position certain certain certain sequence position certain false p.Asp140Tyr variant variant certain certain sequence position certain certain certain sequence position certain false p.Asn151Lys variant variant certain certain sequence position certain certain certain sequence position certain false p.Glu176Val variant variant certain certain sequence position certain certain certain sequence position certain false p.Leu180Gln variant variant certain certain sequence position certain certain certain sequence position certain false p.Asp185Glu variant variant certain certain sequence position certain certain certain sequence position certain false p.Glu190_Trp191delinsAspGly variant variant certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3678201 unspecified role unspecified role neutral component neutral component purified purified region sufficient to bind sufficient binding region sufficient to bind range range range range false ecoli Escherichia coli (strain K12) physical association physical association false false false 2 In the absence of peptide there is no interaction. HLA-A*2402 b2m-hla_a-3 3678198 N/A 3678202 unspecified role unspecified role neutral component neutral component N1 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 3678200 unspecified role unspecified role neutral component neutral component purified purified partial_ecd sufficient to bind sufficient binding region sufficient to bind range range range range false p.Phe33Ser variant variant certain certain sequence position certain certain certain sequence position certain false p.Gln86Glu variant variant certain certain sequence position certain certain certain sequence position certain false p.Arg89_Asn90delinsGlyLys variant variant certain certain sequence position certain certain certain sequence position certain false p.Gln94His variant variant certain certain sequence position certain certain certain sequence position certain false p.Val100_Asp101delinsGluAsn variant variant certain certain sequence position certain certain certain sequence position certain false p.Gly103_Gly107delinsArgIleAlaLeuArg variant variant certain certain sequence position certain certain certain sequence position certain false p.Ile119Leu variant variant certain certain sequence position certain certain certain sequence position certain false p.Ile121Met variant variant certain certain sequence position certain certain certain sequence position certain false p.Tyr123Phe variant variant certain certain sequence position certain certain certain sequence position certain false p.Arg138His variant variant certain certain sequence position certain certain certain sequence position certain false p.Asp140Tyr variant variant certain certain sequence position certain certain certain sequence position certain false p.Asn151Lys variant variant certain certain sequence position certain certain certain sequence position certain false p.Glu176Val variant variant certain certain sequence position certain certain certain sequence position certain false p.Leu180Gln variant variant certain certain sequence position certain certain certain sequence position certain false p.Asp185Glu variant variant certain certain sequence position certain certain certain sequence position certain false p.Glu190_Trp191delinsAspGly variant variant certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3678201 unspecified role unspecified role neutral component neutral component purified purified region sufficient to bind sufficient binding region sufficient to bind range range range range false ecoli Escherichia coli (strain K12) physical association physical association false false false Table 3 In the absence of peptide there is no interaction. HLA-A*2402