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/ fisher-2007-1 Structural and biochemical studies of ALIX/AIP1 and its role in retrovirus budding. in vitro In vitro spr surface plasmon resonance Optical biosensor BIAcore(r) BIAcore(r) Optical biosensor spr predetermined predetermined participant predetermined Fisher RD., Chung HY., Zhai Q., Robinson H., Sundquist WI., Hill CP. Apoptosis - Interactions involving proteins with a function related to apoptosis To find the position of YP->SR mutations in Gag proteins the motif YPXnL was searched for (where n= 1-3). Only one site was found in each protein. For the Gag proteins, in each case there were different UniProt entries corresponding to different viral isolates in each case the longest was taken and where there were 2 of equal longest length the first in the list was taken. wes@biochem.utah.edu,chris@biochem.utah.edu Cell (0092-8674) 2007 Only protein-protein interactions 8 imex curation Synapse - Interactions of proteins with an established role in the presynapse. fisher-2007-3 Structural and biochemical studies of ALIX/AIP1 and its role in retrovirus budding. yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Fisher RD., Chung HY., Zhai Q., Robinson H., Sundquist WI., Hill CP. Apoptosis - Interactions involving proteins with a function related to apoptosis To find the position of YP->SR mutations in Gag proteins the motif YPXnL was searched for (where n= 1-3). Only one site was found in each protein. For the Gag proteins, in each case there were different UniProt entries corresponding to different viral isolates in each case the longest was taken and where there were 2 of equal longest length the first in the list was taken. wes@biochem.utah.edu,chris@biochem.utah.edu Cell (0092-8674) 2007 Only protein-protein interactions 8 imex curation Synapse - Interactions of proteins with an established role in the presynapse. fisher-2007-2 Structural and biochemical studies of ALIX/AIP1 and its role in retrovirus budding. in vitro In vitro pull down pull down predetermined predetermined participant predetermined Fisher RD., Chung HY., Zhai Q., Robinson H., Sundquist WI., Hill CP. Apoptosis - Interactions involving proteins with a function related to apoptosis To find the position of YP->SR mutations in Gag proteins the motif YPXnL was searched for (where n= 1-3). Only one site was found in each protein. For the Gag proteins, in each case there were different UniProt entries corresponding to different viral isolates in each case the longest was taken and where there were 2 of equal longest length the first in the list was taken. wes@biochem.utah.edu,chris@biochem.utah.edu Cell (0092-8674) 2007 Only protein-protein interactions 8 imex curation Synapse - Interactions of proteins with an established role in the presynapse. gag_hv1b1 Gag polyprotein gag Pr55Gag protein protein hv1b1 Human immunodeficiency virus type 1 group M subtype B (isolate BH10) (HIV-1) HIV-1 MGARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQTGSEELRSLYNTVATLYCVHQRIEIKDTKEALDKIEEEQNKSKKKAQQAAADTGHSSQVSQNYPIVQNIQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVLAEAMSQVTNTATIMMQRGNFRNQRKMVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWPSYKGRPGNFLQSRPEPTAPPFLQSRPEPTAPPEESFRSGVETTTPPQKQEPIDKELYPLTSLRSLFGNDPSSQ pdc6i_human Programmed cell death 6-interacting protein PDCD6IP AIP1 KIAA1375 ALIX ALG-2-interacting protein 1 Hp95 ALG-2-interacting protein X protein protein human Homo sapiens Human MATFISVQLKKTSEVDLAKPLVKFIQQTYPSGGEEQAQYCRAAEELSKLRRAAVGRPLDKHEGALETLLRYYDQICSIEPKFPFSENQICLTFTWKDAFDKGSLFGGSVKLALASLGYEKSCVLFNCAALASQIAAEQNLDNDEGLKIAAKHYQFASGAFLHIKETVLSALSREPTVDISPDTVGTLSLIMLAQAQEVFFLKATRDKMKDAIIAKLANQAADYFGDAFKQCQYKDTLPKEVFPVLAAKHCIMQANAEYHQSILAKQQKKFGEEIARLQHAAELIKTVASRYDEYVNVKDFSDKINRALAAAKKDNDFIYHDRVPDLKDLDPIGKATLVKSTPVNVPISQKFTDLFEKMVPVSVQQSLAAYNQRKADLVNRSIAQMREATTLANGVLASLNLPAAIEDVSGDTVPQSILTKSRSVIEQGGIQTVDQLIKELPELLQRNREILDESLRLLDEEEATDNDLRAKFKERWQRTPSNELYKPLRAEGTNFRTVLDKAVQADGQVKECYQSHRDTIVLLCKPEPELNAAIPSANPAKTMQGSEVVNVLKSLLSNLDEVKKEREGLENDLKSVNFDMTSKFLTALAQDGVINEEALSVTELDRVYGGLTTKVQESLKKQEGLLKNIQVSHQEFSKMKQSNNEANLREEVLKNLATAYDNFVELVANLKEGTKFYNELTEILVRFQNKCSDIVFARKTERDELLKDLQQSIAREPSAPSIPTPAYQSSPAGGHAPTPPTPAPRTMPPTKPQPPARPPPPVLPANRAPSATAPSPVGAGTAAPAPSQTPGSAPPPQAQGPPYPTYPGYPGYCQMPMPMGYNPYAYGQYNMPYPPVYHQSPGQAPYPGPQQPSYPFPQPPQQSYYPQQ gag_eiav9 Gag polyprotein gag protein protein eiav9 Equine infectious anemia virus (isolate 1369) (EIAV) MGDPLTWSKALKKLEKVTVQGSQKLTTGNCNWALSLVDLFHDTNFVKEKDWQLRDVIPLLEDVTQTLSGQEREAFERTWWAISAVKMGLQINNVVDGKASFQLLRAKYEKKTANKKQSEPSEEYPIMIDGAGNRNFRPLTPRGYTTWVNTIQTNGLLNEASQNLFGILSVDCTSEEMNAFLDVVPGQAGQKQILLDAIDKIADDWDNRHPLPNAPLVAPPQGPIPMTARFIRGLGVPRERQMEPAFDQFRQTYRQWIIEAMSEGIKVMIGKPKAQNIRQGAKEPYPEFVDRLLSQIKSEGHPQEISKFLTDTLTIQNANEECRNAMRHLRPEDTLEEKMYACRDIGTTKQKMMLLAKALQTGLAGPFKGGALKGGPLKAAQTCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRSVPKNGKQGAQGRPQKQTFPIQQKSQHNKSVVQETPQTQNLYPDLSEIKKEYNVKEKDQVEDLNLDSLWE ts101_human Tumor susceptibility gene 101 protein TSG101 ESCRT-I complex subunit TSG101 protein protein human Homo sapiens Human MAVSESQLKKMVSKYKYRDLTVRETVNVITLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFSRPISASYPPYQATGPPNTSYMPGMPGGISPYPSGYPPNPSGYPGCPYPPGGPYPATTSSQYPSQPPVTTVGPSRDGTISEDTIRASLISAVSDKLRWRMKEEMDRAQAELNALKRTEEDLKKGHQKLEEMVTRLDQEVAEVDKNIELLKKKDEELSSALEKMENQSENNDIDEVIIPTAPLYKQILNLYAEENAIEDTIFYLGEALRRGVIDLDVFLKHVRLLSRKQFQLRALMQKARKTAGLSDLY sh3g2_human Endophilin-A1 SH3GL2 CNSA2 SH3D2A Endophilin-1 SH3 domain-containing GRB2-like protein 2 SH3 domain protein 2A EEN-B1 protein protein human Homo sapiens Human MSVAGLKKQFHKATQKVSEKVGGAEGTKLDDDFKEMERKVDVTSRAVMEIMTKTIEYLQPNPASRAKLSMINTMSKIRGQEKGPGYPQAEALLAEAMLKFGRELGDDCNFGPALGEVGEAMRELSEVKDSLDIEVKQNFIDPLQNLHDKDLREIQHHLKKLEGRRLDFDYKKKRQGKIPDEELRQALEKFDESKEIAESSMFNLLEMDIEQVSQLSALVQAQLEYHKQAVQILQQVTVRLEERIRQASSQPRREYQPKPRMSLEFPTGDSTQPNGGLSHTGTPKPSGVQMDQPCCRALYDFEPENEGELGFKEGDIITLTNQIDENWYEGMLHGHSGFFPINYVEILVALPH sh3g1_human Endophilin-A2 Endophilin-2 SH3 domain-containing GRB2-like protein 1 SH3 domain protein 2B Extra eleven-nineteen leukemia fusion gene protein EEN fusion partner of MLL SH3GL1 CNSA1 SH3D2B protein protein human Homo sapiens Human MSVAGLKKQFYKASQLVSEKVGGAEGTKLDDDFKEMEKKVDVTSKAVTEVLARTIEYLQPNPASRAKLTMLNTVSKIRGQVKNPGYPQSEGLLGECMIRHGKELGGESNFGDALLDAGESMKRLAEVKDSLDIEVKQNFIDPLQNLCEKDLKEIQHHLKKLEGRRLDFDYKKKRQGKIPDEELRQALEKFEESKEVAETSMHNLLETDIEQVSQLSALVDAQLDYHRQAVQILDELAEKLKRRMREASSRPKREYKPKPREPFDLGEPEQSNGGFPCTTAPKIAASSSFRSSDKPIRTPSRSMPPLDQPSCKALYDFEPENDGELGFHEGDVITLTNQIDENWYEGMLDGQSGFFPLSYVEVLVPLPQ 6E5BE978BC955077 chm4a_human Charged multivesicular body protein 4a Chromatin-modifying protein 4a Vacuolar protein sorting-associated protein 32-1 SNF7-1 SNF7 homolog associated with Alix-2 CHMP4A C14orf123 SHAX2 CDA04 HSPC134 protein protein human Homo sapiens Human MSGLGRLFGKGKKEKGPTPEEAIQKLKETEKILIKKQEFLEQKIQQELQTAKKYGTKNKRAALQALRRKKRFEQQLAQTDGTLSTLEFQREAIENATTNAEVLRTMELAAQSMKKAYQDMDIDKVDELMTDITEQQEVAQQISDAISRPMGFGDDVDEDELLEELEELEQEELAQELLNVGDKEEEPSVKLPSVPSTHLPAGPAPKVDEDEEALKQLAEWVS pdcd6ip-gag ALIX V domain binds HIV-1 p6Gag in biosensor binding experiments 599315 N/A 599318 unspecified role unspecified role prey prey ecobb Escherichia coli (strain B / BL21) N/A 599319 unspecified role unspecified role bait bait region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false Q8WUM4:p.Val498Asp mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false Q8WUM4:p.Phe676Asp mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false Q8WUM4:p.Ile683Asp mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecobb Escherichia coli (strain B / BL21) physical association physical association false false false 3 A, Table S2 pdcd6ip-gag-1 ALIX V domain binds HIV-1 p6Gag in biosensor binding experiments 599315 N/A 599318 unspecified role unspecified role prey prey P03347:p.Tyr496_Pro497delinsSerArg mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false ecobb Escherichia coli (strain B / BL21) N/A 599319 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobb Escherichia coli (strain B / BL21) physical association physical association false false false 3 A, Table S2 The mutation of YP to SR in the Gag YPX(n)L late domain reduced binding affinity substantially (over 15-fold). pdcd6ip-gag-2 ALIX V domain binds EIAV p9Gag in biosensor binding experiments 599315 N/A 599320 unspecified role unspecified role prey prey P69730:p.[Tyr458Ser;Pro459Arg] mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecobb Escherichia coli (strain B / BL21) N/A 599319 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobb Escherichia coli (strain B / BL21) physical association physical association false false false 3 A, Table S2 The mutation of YP to SR in the Gag YPX(n)L late domain reduced binding affinity substantially (over 15-fold). pdcd6ip-gag-3 ALIX V domain binds E1AV p9Gag in biosensor binding experiments 599315 N/A 599320 unspecified role unspecified role prey prey ecobb Escherichia coli (strain B / BL21) N/A 599319 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false Q8WUM4:p.Val498Asp mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false Q8WUM4:p.Phe676Asp mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false Q8WUM4:p.Ile683Asp mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false ecobb Escherichia coli (strain B / BL21) physical association physical association false false false 3 A, Table S2 ALIX V (V498D) Kd =1.8 E-9 M; ALIX V (I593D) 5.8 E-7 M. pdcd6ip-tsg101 TSG101 UEV domain binds ALIX714-723 in a biosensor assay 599315 N/A 599319 unspecified role unspecified role bait bait Q8WUM4:p.Pro720Leu mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecobb Escherichia coli (strain B / BL21) N/A 599321 unspecified role unspecified role prey prey n-terminal UEV domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false S5 A The mutation Pro720Leu in the PSAP motif of ALIX714-723 eliminates binding to TSG101 UEV domain. pdcd6ip-sh3gl2 ALIX binds endophilin-1 in a yeast two-hybrid assay 599316 N/A 599322 unspecified role unspecified role bait bait N/A 599319 unspecified role unspecified role prey prey Q8WUM4:p.[Arg757Ala;Pro758Ala] mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false S5 B pdcd6ip-sh3gl1 ALIX binds endophilin-2 in a yeast two-hybrid assay 599316 N/A 599319 unspecified role unspecified role prey prey Q8WUM4:p.[Arg757Ala;Pro758Ala] mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false N/A 599323 unspecified role unspecified role bait bait physical association physical association false false false S5 B pdcd6ip-chmp4a GST-CHMP4A pulls down ALIXBro1 in vitro 599317 N/A 599319 unspecified role unspecified role prey prey n-terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false Q8WUM4:p.Ile212Asp mutation disrupting mutation disrupting interaction mutation disrupting mutation analysis mutation analysis certain certain sequence position certain certain certain sequence position certain false ecobb Escherichia coli (strain B / BL21) N/A 599324 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 6 B