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/ ren-2009-3 A structure-based mechanism for vesicle capture by the multisubunit tethering complex Dsl1. in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Ren Y., Yip CK., Tripathi A., Huie D., Jeffrey PD., Walz T., Hughson FM. hughson@princeton.edu Cell (0092-8674) 2009 Only protein-protein interactions 8 imex curation ren-2009-2 A structure-based mechanism for vesicle capture by the multisubunit tethering complex Dsl1. in vitro In vitro electron microscopy electron microscopy Electron crystallography Electron cryomicroscopy Electron crystallography Electron cryomicroscopy predetermined predetermined participant predetermined Ren Y., Yip CK., Tripathi A., Huie D., Jeffrey PD., Walz T., Hughson FM. hughson@princeton.edu Cell (0092-8674) 2009 Only protein-protein interactions 8 imex curation ren-2009-1 A structure-based mechanism for vesicle capture by the multisubunit tethering complex Dsl1. in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Ren Y., Yip CK., Tripathi A., Huie D., Jeffrey PD., Walz T., Hughson FM. hughson@princeton.edu Cell (0092-8674) 2009 Only protein-protein interactions 8 imex curation sec39_yeast Protein transport protein SEC39 Dependent on SLY1-20 protein 3 SEC39 DSL3 YLR440C protein protein yeast Saccharomyces cerevisiae Baker's yeast MLEEQLYLLACIFASRADTRNIKKLSTRLGSQSKYLEILCVLWPELDDPKNLLFLRELEEEVQSPEGEETTDEDVIVELLESDSSLIPLIESDTTTRSNRYHELQEFISKKLNNKTLENFEEWLRERILICNEMIPETPLLYSVLWETAKSKVLSTKFIGWVEGVLKPLDHLNKRLHLIFKINEWEKMPDSELFKIIFDGVEDMQGYIGIADVIEDELAPTLSYGKKWETFITEFFNKQQFSLKSDTNYQLFIKLYYSLEKGVKDNSEASRKLQSNVVDILFHNSENLFNLSSLTHKLDELWSILSGFPDEITIEEQKTITALEMKQFMEFFIKCSTKFSFKEIFAITQEEESAQLAHFSSLCHEEFNKANEISSFLQAMYETVLDISKDDKIFTRISMDEKLYSILEILLQMNEFAYIEAIIERFDYSNNTQIYELLVKFFWHFFNNASNGLRKEPEMKKASQTLQIIQKHMSQRAGTNLTKLEVLLEISDKLSHYSINLNKSHNGARDTAFKPSNILEYRDCPLDIISNLLELNPRLYKDLPTTKSLLFGIYDSLSINREGQTGKVEVDLMVLHIDYALVNLDFGTAYELGKQVFEICQEAGQHMMKALGDEHWLTFYQMGKFVDPNWVDNEIPTEIIVLQMSILGRLLEVCPLEEVEIVTSQWSTLELELSARDLVKDKYALDGQNDNKSKVGGIAREIFHNVTNF 8ABD59328A006863 use1_yeast Protein transport protein USE1 USE1 SLT1 Unconventional SNARE in the endoplasmic reticulum protein 1 SNARE-like tail-anchored protein 1 YGL098W protein protein yeast Saccharomyces cerevisiae Baker's yeast MAETSNDPFLSYVLSSKQLTNLNRLRRKAVTKQLGSSDDNKVSEEFLRYQHTYQREAFEYLQTKHDAHKIMESQYEQYQSSSKTRRYSIDLDSVDAVDTESQTEYPNEEFIDRNEDSEAVMELRKRLLGKGQNKGLGYETTKSVDRQIEDQDTLQQDLIQDMSKLVGSLKQGAVAFQSALDEDKQVLGAAEIGIQVASQGLMDVSGKLRKYDKSKLSYLFYITVFIFMILGLVFTFIIIQLFPAL 213ABBF0492E80EF tip20_yeast Protein transport protein TIP20 YGL145W TIP20 TIP1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MNGIDDLLNINDRIKQVQNERNELASKLQNLKQSLASNDTEVALSEVIAQDIIEVGASVEGLEQLRAKYGDLQILNKLEKVAVQQTQMQAGVDKLDSFERQLDELAEQPPDQFTLDDVKALHSKLTSVFATVPQINNIDSQYAAYNKLKSKVTGKYNDVIIQRLATNWSNTFDQKLLEAQWDTQKFASTSVGLVKCLRENSTKLYQLSLLYLPLEEETQNGDSERPLSRSNNNQEPVLWNFKSLANNFNVRFTYHFHATSSSSKIETYFQFLNDYLAENLYKCINIFHDDCNGLTKPVIHEQFINYVLQPIRDKVRSTLFQNDLKTLIVLISQILATDKNLLNSFHYHGLGLVSLISDEVWEKWINYEVEMANRQFINITKNPEDFPKSSQNFVKLINKIYDYLEPFYDLDFDLLVRYKLMTCSLIFMNLTSSYLDYILTVDSLNETRTKEQELYQTMAKLQHVNFVYRKIKSLSSNFIFIQLTDIVNSTESKKYNSLFQNVENDYEKAMSTDMQNSIVHRIQKLLKETLRNYFKISTWSTLEMSVDENIGPSSVPSAELVNSINVLRRLINKLDSMDIPLAISLKVKNELLNVIVNYFTESILKLNKFNQNGLNQFLHDFKSLSSILSLPSHATNYKCMSLHELVKILKLKYDPNNQQFLNPEYIKTGNFTSLKEAYSIKYLKDTKIQDALYRIIYGNIL 3E561DD4C0B9C176 sec20_yeast Protein transport protein SEC20 SEC20 D9719.4 YDR498C protein protein yeast Saccharomyces cerevisiae Baker's yeast MVVTFLQDLEVLQDALLNNLQKLSAISRRKESGESKHDNKDSFAAIANEHNDEEEEIEFEDLVNIIESKVSDFESVLKCSIVEMTYKYPELKLQWEKSPRYDQCDKLHIVKLDKQMNEDIYAQLVEELDFVLQFVDWFYCYRLKVKEILRQHHKRDLAWNDEKRDRAIKFHAVDYDKLHQGTSSSSSLTSTSMEKASTREKLLSKTKQLTNNLVRGNQILQSGILQSDLNLDELRAQTNSLTQIDDKYTQFETVFKKTADLVKVLENASHQEKRDVYLSLGFLLCCVSWVLWRRIFKLPVKLGLWLLFKFFKGILVTLGLVKSYAGSSSSLQAPSLVLNAPILATTTTSSATSVEPFASVSAVSSIQRAVDEAVDRIVSHDEL 9BF8C748B8A8F589 ufe1_yeast Syntaxin UFE1 UFE1 YOR29-26 YOR075W protein protein yeast Saccharomyces cerevisiae Baker's yeast MMSDLTPIFRKYVAVIDDARNEQNGIDDHVERKQEDFGNSNETCEMFRDSFIKECARLLKFLVELNKVIKQIEKNYLDDFNMSDAEKDEFDMECRLQIQQYFKKFEFLENYEMERHNLSLKRFQSKSHRWSKILSNKNDNTKHVIHPQDIENGVYEFRLGVLRCLNLWIKYVSSKFTTIQQERLILENKMNFNSTPMPTLSNNADDFSADAIDISVSQSAPVETVQDEVKHYEETISKLTQEQLQVLETEHSELLNQKNEQLKKVETINKTILDIVNIQNELSNHLTVQSQNINLMLNNQDDIELNIKKGNKELRKAKRAAGRTAKMTTYGAIIMGVFILFLDYVG sec22_yeast Protein transport protein SEC22 SEC22 SLY2 YLR268W L8479.3 TSL26 Suppressor of loss of YPT1 protein 2 protein protein yeast Saccharomyces cerevisiae Baker's yeast MIKSTLIYREDGLPLCTSVDNENDPSLFEQKQKVKIVVSRLTPQSATEATLESGSFEIHYLKKSMVYYFVICESGYPRNLAFSYLNDIAQEFEHSFANEYPKPTVRPYQFVNFDNFLQMTKKSYSDKKVQDNLDQLNQELVGVKQIMSKNIEDLLYRGDSLDKMSDMSSSLKETSKRYRKSAQKINFDLLISQYAPIVIVAFFFVFLFWWIFLK 9FA3E34EAAFB9536 dsl1_yeast Protein transport protein DSL1 Dependent on SLY1-20 protein 1 YNL258C N0842 DSL1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MESLFPNKGEIIRELLKDPLILKNDSKRSNGSELELDSSDLLQREAILANELNILDNLKTFLNLIKEVKTNLNILELENCYYSLQSLRKKMRNNAAYLKQSFNFQQSISTYVDTLHLELVSTLYKILTNGFWKITENSIQFTPTVEWGKDKVHIEYDTFMDFVAQQYFPKGSLDNQAWFILDMTSADSQEQVRAKLNTIMKEYMNLSRIVSMIKNSIFISGKEISYENEKNILVFSKSSSHGQHCVSTVLTSFEAVCDFMLDGLAFRDRKTLSYELGPLFNTEFTKFVKNNASIILESLDSPLKNLVSVINNKLTRLVAKSEVTNWTHSGKEIQDLLMNKQLYYNLLLDKVLESHISEIRSIFEDPKKSWQNLEVVELTTSNTNTMSEKIGKNDSDVQNEKELHNAVSKDDDWNWEVEDDDADAWGDEIDVNIDDEEEKTNQEKEKEPEEEENAWDEAWAIDENIDDASLENGKEHLKAHDVGSLDKDHIEVTQLPKLFLAISQNFKSSFADSHVDEQYFAYKYNLLQTSYMAMCTANFSHNWCQLYVDMRYLIERDEKLYRIKELTRNLLETKLNMKYRIVCQLIRHQLTEFRENERNPSWDATIEKLLPYILKEIVRPLQKIRGEEGSRYLLSFLNFLYNDCVTKEILKWQIISEVNSENLGELVSLLVNNTDIQLLAKEPSYKKMREKFATMGKFLPLHLKEIMEMFYNGDFYLFATDELIQWIELLFADTPLRRNAIDDIYEIRGTALDD 51EDB17F2C55A917 q6cus2_klula KLLA0_C02695g protein protein klula Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) Yeast Candida sphaerica MATLEKLLNDLLSDTSALSQAIEADPQFKSSDSVHPKPNSKLLEEVLREDSDLTKDLAKYNQYKILSDLLKEFNTNYELNELENCYYSLQNIHKKFKDVNISGESFRFQQSVATYIDCLHLNVLERFKEVSNMFYTISGNEMMFKKTIELDSVEFNFDEMVELFENNFFDHNMIDQTHWFIASTNLETYKDKEIVLLQEILDDTVKLNPLIKFFKEFVFDEKCIMVRAEPGKLTLATSEYNSLDQIKSYQTLTTFIENDLSKHAKESVMIHFGNVLLTELLKIIRANPELLSNDKEQTTEIISSIHDSLTKISEETEWAYDGFELNRILKDENIYTTLKFESMMQQRVIQIRSIPEEEYHELVSVQFKTDGGKYEKGEKQDLELSEKKTENGKDTESWGWNENQDSDEHDGWDEELDIDVDNVPIQVSVFVQSAAKVFTEFEQGCDTIGRSKVESIYLYKFNLLQTAFFAMVSEKVNDWTQLYKDVRYLYTENPKLLQLMELNSRRLDLNLNLIKKTIYKLVNDQLQELKDNERTPDWDITISSLLPYLKKTALPTLYKLEDNTILVALIRYIVHDLVIDNILHWRVISEKSSENLSEFIMLLLSGLEIPRLNLIETYRHSREKLGILSKILTAHLKDILEMFYEGEFFLFETDEIVQWIILLFADTPTRRDCIDEIRRVREEATD sec39-use1 Binding of Sec39 to USE1 demonstrated by gel filtration 867636 n/a 867639 unspecified role unspecified role neutral component neutral component n-terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 867640 unspecified role unspecified role neutral component neutral component n-terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region trigger factor fusion protein fusion protein undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) 867651 867649 direct interaction direct interaction false false false Fig. 3A sec39-use1-1 Binding of Sec39 to USE1 demonstrated by gel filtration 867636 n/a 867640 unspecified role unspecified role neutral component neutral component n-terminal required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false region trigger factor fusion protein fusion protein undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) n/a 867639 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Fig. 3B, 3C tip20-sec20-2 Interaction between Sec20 and Tip20 demonstrated by gel filtration 867636 n/a 867641 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) n/a 867642 unspecified role unspecified role neutral component neutral component region required to bind necessary binding region required to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Fig. 3D, 3E use1-sec20-1 Interaction between Use1, Ufe1, Sec20 and Sec22 demonstrated by gel filtration 867636 n/a 867642 unspecified role unspecified role neutral component neutral component cytoplasmic region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 867640 unspecified role unspecified role neutral component neutral component cytoplasmic region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 867643 unspecified role unspecified role neutral component neutral component snare region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 867644 unspecified role unspecified role neutral component neutral component snare region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) physical association physical association false false false Fig. 4A Sec39 was added to the pre-mix to solubulise Use1 but was not shown to be present in the assembled complex. use1-sec20-2 Interaction between Use1, Ufe1, Sec20 and Sec22 demonstrated by gel filtration 867636 n/a 867640 unspecified role unspecified role neutral component neutral component cytoplasmic region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 867644 unspecified role unspecified role neutral component neutral component snare region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 867642 unspecified role unspecified role neutral component neutral component cytoplasmic region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 867645 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) n/a 867639 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) n/a 867643 unspecified role unspecified role neutral component neutral component snare region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 867641 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) physical association physical association false false false Fig. 4C dsl1-sec39-2 Interaction between Sec39 and Dsl1 demonstrated by electron microscopy 867637 n/a 867639 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) n/a 867645 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Fig. 2B dsl1-sec39-3 Interaction between Sec39, Tip20 and Dsl1 demonstrated by electron microscopy 867637 n/a 867645 unspecified role unspecified role neutral component neutral component dsl1_yeast binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false dsl1_yeast binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 867641 unspecified role unspecified role neutral component neutral component tip20_yeast binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 867639 unspecified role unspecified role neutral component neutral component sec39_yeast binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) 867691 867689 867693 867688 direct interaction direct interaction false false false Supp. Fig. 2C The Tip20-Dsl1 interaction was stabilized by an engineered disulphide bond between Tip20 L28C and Dsl1 L48C. dsl1-sec39-1 Interaction between Sec39 and Dsl1 demonstrated by X-ray crystallography 867638 n/a 867646 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 867639 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 2.6A R working 20.5%, R free 27.1 Supp. Table 1